diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..823b334
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,7 @@
+falmeida_py.egg-info/
+dist
+falmeida_py/__pycache__
+build/*
+docs/_build
+PHD_FILES
+test*
\ No newline at end of file
diff --git a/.gitpod.yml b/.gitpod.yml
new file mode 100644
index 0000000..a565aba
--- /dev/null
+++ b/.gitpod.yml
@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+vscode:
+ extensions: # based on nf-core.nf-core-extensionpack
+ - codezombiech.gitignore # Language support for .gitignore files
+ # - cssho.vscode-svgviewer # SVG viewer
+ - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+ - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
+ - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+ - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+ - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
+ # - nextflow.nextflow # Nextflow syntax highlighting
+ - oderwat.indent-rainbow # Highlight indentation level
+ - streetsidesoftware.code-spell-checker # Spelling checker for source code
\ No newline at end of file
diff --git a/.vscode/settings.json b/.vscode/settings.json
new file mode 100644
index 0000000..12ff2fd
--- /dev/null
+++ b/.vscode/settings.json
@@ -0,0 +1,3 @@
+{
+ "restructuredtext.confPath": "${workspaceFolder}/docs"
+}
\ No newline at end of file
diff --git a/CHANGELOG.md b/CHANGELOG.md
new file mode 100644
index 0000000..70413f1
--- /dev/null
+++ b/CHANGELOG.md
@@ -0,0 +1,23 @@
+# Changelog
+
+Started only in version 0.5
+
+## v1.2.3
+
+- Added ICEberg and PHAST results to bacannot json summary file
+
+## v1.2.2
+
+- Added a file size check, only enter bacannot summary creation if results files are not empty
+- Fixed mob_suite summary parsing (added .astype(str))
+- Moved MGE dict key generation for inside the integron_finder loop
+
+## v1.2.1
+
+- Added a quick fix for plasmid finder results parsing, as results from gram-negative have only one database, but for gram-positive it has >1.
+
+## v0.5
+
+### hotfix
+
+A small fix has been performed, the blast databases now in the scripts are created without the `-parse_seqids` option because it was bringing problem in the subset module (`align2subsetgbk`).
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
new file mode 100644
index 0000000..f288702
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,674 @@
+ GNU GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
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+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time. Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+
+ Copyright (C)
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+
+ This program is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see .
+
+Also add information on how to contact you by electronic and paper mail.
+
+ If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+ Copyright (C)
+ This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+ This is free software, and you are welcome to redistribute it
+ under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License. Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+ You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+.
+
+ The GNU General Public License does not permit incorporating your program
+into proprietary programs. If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library. If this is what you want to do, use the GNU Lesser General
+Public License instead of this License. But first, please read
+.
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..d1c3553
--- /dev/null
+++ b/README.md
@@ -0,0 +1,41 @@
+# falmeida-py (Felipe Almeida python scripts)
+
+[](https://anaconda.org/falmeida/falmeida-py)
+[](https://anaconda.org/falmeida/falmeida-py)
+[](https://anaconda.org/falmeida/falmeida-py)
+[](https://falmeida-py.readthedocs.io/en/latest/?badge=latest)
+
+This repository has been turned into an installable python package in order to facilitate the distribution of my custom python scripts and, in turn, make them easier to execute.
+
+Read the complete documentation »
+
+## Installation
+
+Installation is super easy and perhaps not required:
+
+```bash
+# Download
+git clone https://github.com/fmalmeida/pythonScripts.git
+cd pythonScripts
+
+# Run without installing
+python3 falmeida-py-runner.py -h
+
+# Or install with conda and run anywhere
+conda install -c anaconda -c conda-forge -c bioconda -c falmeida falmeida-py
+
+# check installation
+falmeida-py -h
+```
+
+## Old scripts
+
+All my python scripts as single scripts, that may or may not be included in the package are available in the `bkp` folder!
+
+## License
+
+This repository has no warranty and is free to use, modify and share under GNU GENERAL PUBLIC LICENSE version 3.
+
+## Contact
+
+Felipe Almeida
diff --git a/Readme.md b/Readme.md
deleted file mode 100644
index f9bf18d..0000000
--- a/Readme.md
+++ /dev/null
@@ -1,15 +0,0 @@
-# About
-
-This repository was created with the only reason to store my Python Scripts that shall eventually be used more than once.
-
-Feel free to comment some if you believe it can be improved also, feel free to use.
-
-# Contact
-
-## Name
-
-Felipe Marques de Almeida
-
-## Email
-
-falmeida@aluno.unb.br
diff --git a/TEs_vs_shiu-pipeline.py b/bkp/TEs_vs_shiu-pipeline.py
similarity index 100%
rename from TEs_vs_shiu-pipeline.py
rename to bkp/TEs_vs_shiu-pipeline.py
diff --git a/bkp/ask_mongo.py b/bkp/ask_mongo.py
new file mode 100644
index 0000000..a9782f9
--- /dev/null
+++ b/bkp/ask_mongo.py
@@ -0,0 +1,184 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+## Def help message
+"""
+Ask mongo: This command allows you to ask/interrogate the mongo dbs in your machine
+
+usage:
+ ask-mongo.py [ -h|--help ]
+ ask-mongo.py [ --dbpath ] [ --list_dbs ]
+ ask-mongo.py [ --dbpath ] [ --db --list_collections ]
+ ask-mongo.py [ --dbpath ] [ --db --collection ] [ --overview ] [ --subfield --key --val ]
+
+options:
+
+ -h, --help Show this screen
+ --dbpath= Where you have saved your dbs? Data directory of your mongo dbs. [Default: /data/db]
+ --list_dbs List available mongo dbs in your system
+ --db= Mongo DB to be queryed
+ --list_collections Check the available collections in a given database
+ --collection= Collection name (from mongo db) to be queryed
+ --overview Documents in a given collection (from a mongo db)
+ --subfield= Is your key/val inside a subfield (a nested document)? Give the name.
+ --key= Query a collection for documents based on which key?
+ --val= What to search in this key?
+
+example:
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+import sys
+import os
+import re
+from docopt import docopt
+import urllib.request, urllib.parse, urllib.error
+import json
+import pymongo
+from pymongo import MongoClient
+import pathlib
+import pprint
+import random
+from bson.objectid import ObjectId
+
+########################
+### Useful functions ###
+########################
+def start_mongod(db_path):
+
+ try:
+ # Function to start mongo shell if not started yet
+ os.system(f"mongod --dbpath {db_path} --syslog --fork &> /dev/null")
+ except:
+ pass
+
+#########################
+### Check your mongos ###
+#########################
+def check_mongos():
+
+ # Create connection
+ client = MongoClient()
+
+ # Get dbs
+ dbs = client.list_database_names()
+
+ # Print databases
+ print(f"\nThe available mondo dbs found in your system are: {dbs}\n")
+
+ # Close client
+ client.close()
+
+#######################################
+### Check collections in a database ###
+#######################################
+def check_db(db_name):
+
+ # Create connection
+ client = MongoClient()
+
+ # Open Database
+ db = client[db_name]
+
+ # Check available collections
+ cols = db.list_collection_names()
+ print(f"\nAll the available collections found in the {db_name} database are given in the list: {cols}\n")
+
+#############################
+### Overview a collection ###
+#############################
+def collection_overview(db_name, collection_name):
+
+ # Create connection
+ client = MongoClient()
+
+ # Open Database
+ db = client[db_name]
+
+ # Open collection
+ collection = db[collection_name]
+
+ # Count
+ n_docs = collection.count_documents({})
+
+ # Get keys
+ keys = []
+ for doc in collection.find({}):
+ for key in iter(doc.keys()):
+ keys.append(key)
+ keys = list(dict.fromkeys(keys)) # remove duplicates
+
+ # Get one as example
+ ids = []
+ for doc in collection.find({}):
+ ids.append(doc['_id'])
+ example = collection.find_one({'_id': ObjectId(random.choice(ids))})
+
+ # Give overview
+ print(f"When analysing the collection {collection_name} in the database {db_name} we have found a total of {n_docs} documents (entries).")
+ print(f"These are the searcheable keys found in these documents: {keys}.")
+ print(f"They are searcheable and parseable based on its values.")
+ print(f"Here it is an example of one document of the collection:\n")
+ pprint.pprint(example)
+
+####################
+### Get Document ###
+####################
+def get_doc(db_name, collection_name, key, val, subfield):
+
+ # Create connection
+ client = MongoClient()
+
+ # Open Database
+ db = client[db_name]
+
+ # Open collection
+ collection = db[collection_name]
+
+ # Find my document
+ if key == '_id':
+ results = collection.find({ key: ObjectId(val) })
+ elif subfield != None:
+ results = collection.find({ f"{subfield}.{key}" : val })
+ else:
+ results = collection.find({ key: val })
+
+ # Print
+ for doc in results:
+ pprint.pprint(doc)
+
+################
+### Def main ###
+################
+if __name__ == '__main__':
+ args = docopt(__doc__, version='v1.0 by Felipe Marques de Almeida')
+
+ # Start db (if not started)
+ start_mongod(db_path=args['--dbpath'])
+
+ ## Help
+ if args['--help']:
+ print(args.strip())
+
+ ## List dbs
+ elif args['--list_dbs']:
+ check_mongos()
+
+ ## List collections
+ elif args['--list_collections'] and args['--db']:
+ check_db(db_name=args['--db'])
+
+ ## Overview collection
+ elif args['--collection'] and args['--db']:
+ if args['--overview']:
+ collection_overview(db_name=args['--db'], collection_name=args['--collection'])
+ elif args['--key'] and args['--val']:
+ get_doc(db_name=args['--db'], collection_name=args['--collection'], key=args['--key'], val=args['--val'],
+ subfield=args['--subfield'])
+
+ ## None
+ else:
+ print("Missing argument!\n")
+ print(__doc__.strip())
diff --git a/detect_genes_with_pfam.py b/bkp/detect_genes_with_pfam.py
similarity index 100%
rename from detect_genes_with_pfam.py
rename to bkp/detect_genes_with_pfam.py
diff --git a/fetch_genomes_entrez.py b/bkp/fetch_genomes_entrez.py
old mode 100755
new mode 100644
similarity index 100%
rename from fetch_genomes_entrez.py
rename to bkp/fetch_genomes_entrez.py
diff --git a/filter_gff.py b/bkp/filter_gff.py
similarity index 100%
rename from filter_gff.py
rename to bkp/filter_gff.py
diff --git a/gff2json.py b/bkp/gff2json.py
old mode 100755
new mode 100644
similarity index 100%
rename from gff2json.py
rename to bkp/gff2json.py
diff --git a/make_UpSetR_from_tsv.py b/bkp/make_UpSetR_from_tsv.py
old mode 100755
new mode 100644
similarity index 100%
rename from make_UpSetR_from_tsv.py
rename to bkp/make_UpSetR_from_tsv.py
diff --git a/mongoDB_parse_JSON.py b/bkp/mongoDB_parse_JSON.py
old mode 100755
new mode 100644
similarity index 100%
rename from mongoDB_parse_JSON.py
rename to bkp/mongoDB_parse_JSON.py
diff --git a/parse_cardDB.py b/bkp/parse_cardDB.py
old mode 100755
new mode 100644
similarity index 100%
rename from parse_cardDB.py
rename to bkp/parse_cardDB.py
diff --git a/parse_resfamsDB.py b/bkp/parse_resfamsDB.py
old mode 100755
new mode 100644
similarity index 100%
rename from parse_resfamsDB.py
rename to bkp/parse_resfamsDB.py
diff --git a/plot_dna_features.py b/bkp/plot_dna_features.py
similarity index 100%
rename from plot_dna_features.py
rename to bkp/plot_dna_features.py
diff --git a/resources/Kp31_card.tsv b/bkp/resources/Kp31_card.tsv
old mode 100755
new mode 100644
similarity index 100%
rename from resources/Kp31_card.tsv
rename to bkp/resources/Kp31_card.tsv
diff --git a/resources/Kp31_resistance.tsv b/bkp/resources/Kp31_resistance.tsv
old mode 100755
new mode 100644
similarity index 100%
rename from resources/Kp31_resistance.tsv
rename to bkp/resources/Kp31_resistance.tsv
diff --git a/resources/Resfams_metadata.xlsx b/bkp/resources/Resfams_metadata.xlsx
similarity index 100%
rename from resources/Resfams_metadata.xlsx
rename to bkp/resources/Resfams_metadata.xlsx
diff --git a/resources/aro_categories_index.tsv b/bkp/resources/aro_categories_index.tsv
similarity index 100%
rename from resources/aro_categories_index.tsv
rename to bkp/resources/aro_categories_index.tsv
diff --git a/resources/aro_index.tsv b/bkp/resources/aro_index.tsv
similarity index 100%
rename from resources/aro_index.tsv
rename to bkp/resources/aro_index.tsv
diff --git a/rgi2gff.py b/bkp/rgi2gff.py
old mode 100755
new mode 100644
similarity index 100%
rename from rgi2gff.py
rename to bkp/rgi2gff.py
diff --git a/run_blasts.py b/bkp/run_blasts.py
similarity index 100%
rename from run_blasts.py
rename to bkp/run_blasts.py
diff --git a/bkp/splitgbk2fasta.py b/bkp/splitgbk2fasta.py
new file mode 100644
index 0000000..aa94ec0
--- /dev/null
+++ b/bkp/splitgbk2fasta.py
@@ -0,0 +1,121 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+########################
+### Def help message ###
+########################
+"""
+A script meant to subset a genbank annotation file based on alignments
+against a query FASTA file
+
+---
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+Usage:
+ splitgbk2fasta.py
+ splitgbk2fasta.py -h|--help
+ splitgbk2fasta.py -v|--version
+ splitgbk2fasta.py ( --gbk --fasta --out ) [ --minid --mincov --culling_limit ]
+
+Options:
+ -h --help Show this screen.
+ -v --version Show version information
+ -g --gbk= Gbk file for subset
+ -f --fasta= FASTA file for querying the gbk
+ -o --out= Gbk filtered output file
+ --minid= Min. Identity percentage for gene annotation [default: 80]
+ --mincov= Min. Covereage for gene annotation [default: 80]
+ --culling_limit= Blast culling_limit for best hit only [default: 1]
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from docopt import docopt
+from Bio import SeqIO
+from io import StringIO
+import pandas as pd
+import os
+import sys
+
+##########################################
+### Function to convert gbk into fasta ###
+##########################################
+def gbk2fasta(gbk):
+ f=open("tmp_gbk.fa", "a")
+ for seq_record in SeqIO.parse(gbk, 'genbank'):
+ for seq_feature in seq_record.features:
+ if seq_feature.type=="CDS":
+ if 'translation' in seq_feature.qualifiers:
+ print(f">{seq_feature.qualifiers['locus_tag'][0]}", file=f)
+ print(f"{seq_feature.qualifiers['translation'][0]}", file=f)
+ else:
+ start = seq_feature.location.nofuzzy_start
+ end = seq_feature.location.nofuzzy_end
+ tl_table = seq_feature.qualifiers['transl_table'][0]
+ if str(seq_feature.strand) == '-1':
+ my_seq = seq_record.seq[start:end].reverse_complement().translate(table=tl_table)
+ else:
+ my_seq = seq_record.seq[start:end].translate(table=tl_table)
+ seq_feature.qualifiers['translation'] = str(my_seq)
+ print(f">{seq_feature.qualifiers['locus_tag'][0]}", file=f)
+ print(f"{seq_feature.qualifiers['translation'][0]}", file=f)
+
+##############################################################
+### Function to run blast and detect locus_tags that match ###
+##############################################################
+def blastgbk(fasta, culling, minid, mincov):
+ # Outfmt
+ outfmt="6 qseqid qstart qend qlen sseqid sstart send slen evalue length pident gaps gapopen stitle"
+
+ # Run blast
+ os.system(f"makeblastdb -dbtype nucl -in {fasta} -out query_db")
+ os.system(f"tblastn -db query_db -query tmp_gbk.fa -outfmt \"{outfmt}\" -culling_limit {culling} | \
+ awk -v minid={minid} -v mincov={mincov} '{{ if ($11 >= minid && (($10 - $12) / $4 * 100) >= mincov) {{print $0}} }}' > out.blast")
+
+############################################
+### Function to filter gbk based on hits ###
+############################################
+def filtergbk(gbk, out):
+
+ f=open(f"{out}", "w")
+ # Read blast results
+ blast_res = pd.read_csv('out.blast', sep = '\t', header=None)
+
+ # Get locus_tags
+ sel_locus = blast_res.iloc[:, 0].tolist()
+
+ # Subset
+ for seq_record in SeqIO.parse(gbk, 'genbank'):
+
+ cds = [feat for feat in seq_record.features if feat.type == 'CDS']
+ filtered = [ft for ft in cds if ft.qualifiers['locus_tag'][0] in sel_locus]
+ seq_record.features = [i for i in filtered]
+ if len(seq_record.features) > 0:
+ SeqIO.write(seq_record, f, 'gb')
+
+############
+### Main ###
+############
+if __name__ == '__main__':
+ arguments = docopt(__doc__, version='v1.0 by Felipe Marques de Almeida')
+
+ ## Run pipeline
+ if arguments['--gbk'] and arguments['--fasta']:
+
+ # Run
+ gbk2fasta(gbk=arguments['--gbk'])
+ blastgbk(fasta=arguments['--fasta'], culling=arguments['--culling_limit'],
+ minid=arguments['--minid'], mincov=arguments['--mincov'])
+ filtergbk(gbk=arguments['--gbk'], out=arguments['--out'])
+
+ # Clean dir
+ os.system(f"rm tmp_gbk.fa out.blast query_db.n*")
+
+ ## None
+ else:
+ print("Missing mandatory arguments")
+ print("Please, check out the help message")
+ print("")
+ print(arguments)
diff --git a/splitgenbank.py b/bkp/splitgenbank.py
similarity index 100%
rename from splitgenbank.py
rename to bkp/splitgenbank.py
diff --git a/teste.json b/bkp/teste.json
similarity index 100%
rename from teste.json
rename to bkp/teste.json
diff --git a/tgfam_vs_shiu-pipeline.py b/bkp/tgfam_vs_shiu-pipeline.py
similarity index 100%
rename from tgfam_vs_shiu-pipeline.py
rename to bkp/tgfam_vs_shiu-pipeline.py
diff --git a/build_conda.sh b/build_conda.sh
new file mode 100644
index 0000000..d3d0571
--- /dev/null
+++ b/build_conda.sh
@@ -0,0 +1,19 @@
+# make dir
+mkdir -p build
+
+# build conda
+conda build --output-folder build/ conda.recipe
+
+# convert to osx
+conda convert -p osx-64 $(find build -name "falmeida-py*.tar.bz2")
+
+# upload osx
+anaconda upload $(find osx-64 -name "falmeida-py*.tar.bz2") --force
+sleep 140
+anaconda upload $(find build/linux-64 -name "falmeida-py*.tar.bz2") --force
+
+# rm dirs
+rm -rf build osx-64
+
+# save new help message
+bash build_helps.sh
diff --git a/build_helps.sh b/build_helps.sh
new file mode 100644
index 0000000..e4f14bf
--- /dev/null
+++ b/build_helps.sh
@@ -0,0 +1,5 @@
+# save new help message
+python3 falmeida-py-runner.py -h &> docs/help_message.txt
+python3 falmeida-py-runner.py tsv2markdown -h &> docs/tsv2markdown_help.txt
+python3 falmeida-py-runner.py splitgbk -h &> docs/splitgbk_help.txt
+python3 falmeida-py-runner.py align2subsetgbk -h &> docs/align2subsetgbk_help.txt
\ No newline at end of file
diff --git a/conda.recipe/meta.yaml b/conda.recipe/meta.yaml
new file mode 100644
index 0000000..b1e862a
--- /dev/null
+++ b/conda.recipe/meta.yaml
@@ -0,0 +1,46 @@
+package:
+ name: falmeida-py
+ version: '1.2.4'
+
+source:
+ path: ..
+
+build:
+ number: 0
+ script: pip install .
+ entry_points:
+ - processrcmfolder = uconnrcmpy.dataprocessing:process_folder
+
+
+requirements:
+ build:
+ - python>=3.8
+ - setuptools
+ - setuptools-git
+ - pandas
+ - tabulate
+ - docopt
+ - biopython
+ - simplejson
+ - importlib_metadata
+ - pyyaml
+
+ run:
+ - python>=3.8
+ - setuptools
+ - setuptools-git
+ - pandas
+ - tabulate
+ - docopt
+ - biopython
+ - simplejson
+ - importlib_metadata
+ - pyyaml
+
+channels:
+ - anaconda
+ - conda-forge
+ - bioconda
+
+about:
+ home: https://github.com/fmalmeida/gff-toolbox
diff --git a/docs/Makefile b/docs/Makefile
new file mode 100644
index 0000000..d4bb2cb
--- /dev/null
+++ b/docs/Makefile
@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS ?=
+SPHINXBUILD ?= sphinx-build
+SOURCEDIR = .
+BUILDDIR = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+ @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+ @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_static/style.css b/docs/_static/style.css
new file mode 100644
index 0000000..a3df43e
--- /dev/null
+++ b/docs/_static/style.css
@@ -0,0 +1,6 @@
+.wy-nav-content {
+ max-width: 100% !important;
+}
+p {
+ text-align:justify;
+}
diff --git a/docs/align2subsetgbk.rst b/docs/align2subsetgbk.rst
new file mode 100644
index 0000000..06b0cac
--- /dev/null
+++ b/docs/align2subsetgbk.rst
@@ -0,0 +1,45 @@
+.. _align2subsetgbk:
+
+align2subsetgbk
+===============
+
+This script is a little more tricky. What does it do?
+
+1. It takes a genbank file and a (Nucleotide) fasta file
+2. It will align the fasta to the (contig) sequences in the genbank file
+3. Then, it will filter the alignments based on the given thresholds and take the its coordinates
+4. Finally, using these coordinates it will filter the genbank file and output only a subset of the annotation features that is found inside these alignments
+
+CLI help message
+----------------
+
+.. literalinclude:: ./align2subsetgbk_help.txt
+ :language: stdout
+
+Usage
+-----
+
+The usage is super simple:
+
+.. code-block:: none
+
+ falmeida-py align2subsetgbk \
+ --gbk sample.gbk \
+ --fasta genomic_islands.fna \
+ --extension 50 \
+ --culling_limit 2
+
+ Processing file: annotation/sample.gbk!
+ qseqid qstart qend qlen sseqid sstart send slen evalue length pident gaps gapopen bitscore
+ 0 NC_016845.1_1287077_1326610 1 39533 39533 NC_016845.1 1287078 1326610 5333942 0.0 39533 100.0 0 0 73004
+ 1 NC_016845.1_1778390_1811349 1 32959 32959 NC_016845.1 1778391 1811349 5333942 0.0 32959 100.0 0 0 60864
+ 2 NC_016845.1_2286181_2305760 1 19579 19579 NC_016845.1 2286182 2305760 5333942 0.0 19579 100.0 0 0 36156
+ 3 NC_016845.1_4049987_4083106 1 33119 33119 NC_016845.1 4049988 4083106 5333942 0.0 33119 100.0 0 0 61160
+ 4 NC_016845.1_4821157_4858652 1 37495 37495 NC_016845.1 4821158 4858652 5333942 0.0 37495 100.0 0 0 69241
+
+
+.. note::
+
+ This command will align the genomic islands to the genbank to find the annotation features that are found inside the regions that align to these genomic islands.
+
+ In the example, the alignments coordinates will be "extendend" 50nt in both directions and, the two best alignments will be used for each sequence (from fasta).
\ No newline at end of file
diff --git a/docs/align2subsetgbk_help.txt b/docs/align2subsetgbk_help.txt
new file mode 100644
index 0000000..769c2b2
--- /dev/null
+++ b/docs/align2subsetgbk_help.txt
@@ -0,0 +1,44 @@
+A script meant to subset a genbank annotation file based on alignments against a query (Nucleotide) FASTA file
+
+---
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+Usage:
+ falmeida-py align2subsetgbk [ -h|--help ]
+ falmeida-py align2subsetgbk [ --gbk --fasta --out --minid --mincov --culling_limit --extension ]
+
+Options:
+ -h --help Show this screen.
+ -g --gbk= Gbk file for subset
+ -f --fasta= FASTA (nucl) file for querying the gbk
+ -o --out= Gbk filtered output file [Default: out.gbk].
+ --extension= Base pair length to extend the flank regions in the alignment [Default: 0].
+ --minid= Min. Identity percentage for gene annotation [Default: 80].
+ --mincov= Min. Covereage for gene annotation [Default: 80].
+ --culling_limit= Blast culling_limit for best hit only [Default: 1].
+falmeida-py: a package to the simple distribution of my custom scripts.
+
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
+ falmeida-py [ -h|--help ] [ ... ]
+
+options:
+ -h --help Show this screen
+ -v --version Show version information
+ --license Show LEGAL LICENSE information
+
+commands:
+ tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
+ splitgbk Command to split multisequence genbank files into individual files.
+ align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
+ gbk2fasta Command to convert genbank files to fasta files.
+ blasts Command to execute automatized blast commands.
+ replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
+ mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
+ bacannot2json Command to summarize main bacannot annotation results into JSON file
+
+Use: `falmeida-py -h` to get more help and see examples.
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000..52a2469
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,115 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'falmeida-py'
+copyright = '2020, Felipe, Almeida. falmeida-py: A simple package to index my frequently used python scripts.'
+author = 'Felipe Marques de Almeida'
+
+
+# -- General configuration ---------------------------------------------------
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+ "sphinx.ext.intersphinx",
+ "sphinx.ext.autodoc",
+ "sphinx.ext.mathjax",
+ "sphinx.ext.viewcode",
+ "sphinx_copybutton"
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages. See the documentation for
+# a list of builtin themes.
+#
+
+# --- default ---
+#import sphinx_rtd_theme
+#html_theme = 'sphinx_rtd_theme'
+
+# --- material ---
+#import sphinx_materialdesign_theme
+#html_theme = "sphinx_materialdesign_theme"
+
+# --- jupyter ---
+#import jupyter_sphinx_theme
+#html_theme = "jupyter"
+#html_sidebars = {'**': ['sidebartoc.html']}
+#html_theme_path = jupyter_sphinx_theme.get_html_theme_path()
+
+# --- karma ---
+#html_theme = "karma_sphinx_theme"
+
+# --- material ---
+html_theme = "sphinx_material"
+# Material theme options (see theme.conf for more information)
+html_theme_options = {
+
+ # Set the color and the accent color
+ # Primary color. Options are red, pink, purple, deep-purple, indigo, blue, light-blue, cyan, teal, green, light-green, lime, yellow, amber, orange, deep-orange, brown, grey, blue-grey, and white.
+ 'color_primary': 'indigo',
+ #Accent color. Options are red, pink, purple, deep-purple, indigo, blue, light-blue, cyan, teal, green, light-green, lime, yellow, amber, orange, and deep-orange.
+ 'color_accent': 'amber',
+
+ # Visible levels of the global TOC; -1 means unlimited
+ 'globaltoc_depth': 1,
+ # If False, expand all TOC entries
+ 'globaltoc_collapse': True,
+ # If True, show hidden TOC entries
+ 'globaltoc_includehidden': True,
+
+ # logo
+ 'logo_icon': "book",
+
+ # repo info
+ "repo_url": "https://github.com/fmalmeida/pythonScripts",
+ "repo_name": "falmeida-py",
+ "repo_type": "github",
+}
+html_sidebars = {
+ "**": ["globaltoc.html", "localtoc.html", "searchbox.html"]
+}
+
+# --- custom css ---
+html_title = project
+html_static_path = ['_static']
+html_css_files = ['style.css']
+
+# Copy button configuration --------------------------------------------------
+# Source: https://sphinx-copybutton.readthedocs.io/en/latest/
+#copybutton_prompt_text = "$ "
diff --git a/docs/help_message.txt b/docs/help_message.txt
new file mode 100644
index 0000000..6ed5318
--- /dev/null
+++ b/docs/help_message.txt
@@ -0,0 +1,25 @@
+falmeida-py: a package to the simple distribution of my custom scripts.
+
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
+ falmeida-py [ -h|--help ] [ ... ]
+
+options:
+ -h --help Show this screen
+ -v --version Show version information
+ --license Show LEGAL LICENSE information
+
+commands:
+ tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
+ splitgbk Command to split multisequence genbank files into individual files.
+ align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
+ gbk2fasta Command to convert genbank files to fasta files.
+ blasts Command to execute automatized blast commands.
+ replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
+ mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
+ bacannot2json Command to summarize main bacannot annotation results into JSON file
+
+Use: `falmeida-py -h` to get more help and see examples.
diff --git a/docs/images/example.svg b/docs/images/example.svg
new file mode 100644
index 0000000..09c2b8e
--- /dev/null
+++ b/docs/images/example.svg
@@ -0,0 +1,2841 @@
+
+
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000..28003ec
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,50 @@
+.. _index:
+
+falmeida-py (Felipe Almeida python scripts)
+===========================================
+
+This is just a simple repository of python scripts that I use in a daily basis. Some of them are used in my projects, some are just for fun. Thus, in order to provide a better way to use my scripts throughout machines, I decided to create a package with them.
+
+Installation
+------------
+
+Conda package
+"""""""""""""
+
+Users are advised to create separate conda environments
+
+.. code-block:: bash
+
+ # Get the conda package
+ mamba create -n falmeida-py -c anaconda -c conda-forge -c bioconda -c falmeida falmeida-py
+
+.. tip::
+
+ Users are advised to use `mamba `_ since it is faster.
+
+Available features
+------------------
+
+Available features can be visualised with the command line help message:
+
+.. literalinclude:: ./help_message.txt
+ :language: stdout
+
+
+.. note::
+
+ All the commands will have a page describing its usage.
+
+.. toctree::
+ :hidden:
+ :caption: Home
+
+ self
+
+.. toctree::
+ :hidden:
+ :caption: Reference book
+
+ tsv2markdown
+ splitgbk
+ align2subsetgbk
diff --git a/docs/requirements.txt b/docs/requirements.txt
new file mode 100644
index 0000000..9b03960
--- /dev/null
+++ b/docs/requirements.txt
@@ -0,0 +1,9 @@
+Sphinx
+sphinxcontrib-applehelp
+sphinxcontrib-devhelp
+sphinxcontrib-htmlhelp
+sphinxcontrib-jsmath
+sphinxcontrib-qthelp
+sphinxcontrib-serializinghtml
+sphinx-material
+sphinx-copybutton
diff --git a/docs/splitgbk.rst b/docs/splitgbk.rst
new file mode 100644
index 0000000..c2ba08d
--- /dev/null
+++ b/docs/splitgbk.rst
@@ -0,0 +1,27 @@
+.. _splitgbk:
+
+splitgbk
+========
+
+This is a super simple script that performs only one task:
+
+* Given a genbank file with multiple sequences, it splits it into multiple files, each one with one sequence and its related annotation features.
+
+CLI help message
+----------------
+
+.. literalinclude:: ./splitgbk_help.txt
+ :language: stdout
+
+Usage
+-----
+
+The usage is super simple:
+
+.. code-block:: none
+
+ falmeida-py tsv2markdown --gbk multi_contig.gbk --outdir single_contig_gbks
+
+.. note::
+
+ The directory must already exist.
\ No newline at end of file
diff --git a/docs/splitgbk_help.txt b/docs/splitgbk_help.txt
new file mode 100644
index 0000000..f139033
--- /dev/null
+++ b/docs/splitgbk_help.txt
@@ -0,0 +1,38 @@
+A very simple script to split multisequence genbank files into separate files
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py splitgbk
+ falmeida-py splitgbk [ -h|--help ]
+ falmeida-py splitgbk [ --gbk ] [ --outdir ]
+
+options:
+ -h --help Show this screen.
+ -g --gbk= Input genbank file to split into multiple individual files.
+ -o --outdir= Directory (must already exist) in which to write the splitted files [Default: ./].
+falmeida-py: a package to the simple distribution of my custom scripts.
+
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
+ falmeida-py [ -h|--help ] [ ... ]
+
+options:
+ -h --help Show this screen
+ -v --version Show version information
+ --license Show LEGAL LICENSE information
+
+commands:
+ tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
+ splitgbk Command to split multisequence genbank files into individual files.
+ align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
+ gbk2fasta Command to convert genbank files to fasta files.
+ blasts Command to execute automatized blast commands.
+ replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
+ mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
+ bacannot2json Command to summarize main bacannot annotation results into JSON file
+
+Use: `falmeida-py -h` to get more help and see examples.
diff --git a/docs/tsv2markdown.rst b/docs/tsv2markdown.rst
new file mode 100644
index 0000000..3707ffe
--- /dev/null
+++ b/docs/tsv2markdown.rst
@@ -0,0 +1,39 @@
+.. _tsv2markdown:
+
+tsv2markdown
+============
+
+Often I've found myself having to add the contents of TSV (or CSV) files in markdown documents such as jupyter notebooks or rmarkdown documents. The process is very tedious, so I created a super simple script to output the contents so it could just be pasted into these documents.
+
+CLI help message
+----------------
+
+.. literalinclude:: ./tsv2markdown_help.txt
+ :language: stdout
+
+Usage
+-----
+
+The usage is super simple. For example, given the following CSV:
+
+.. code-block:: none
+
+ sample1,brazil,river,2020
+ sample2,argentina,sewer,2020
+ sample3,brazil,sewer,2020
+
+We could rapidply create a markdown table entry with:
+
+.. code-block:: none
+
+ falmeida-py tsv2markdown --csv sample.csv --header "sample id,country,collection source,year"
+
+ | sample id | country | collection source | year |
+ |-------------|-----------|---------------------|--------|
+ | sample1 | brazil | river | 2020 |
+ | sample2 | argentina | sewer | 2020 |
+ | sample3 | brazil | sewer | 2020 |
+
+.. note::
+
+ If the first line of the document (TSV or CSV) is a header, will to not need to use the ``--header`` option, because it will use the frist line as the header.
\ No newline at end of file
diff --git a/docs/tsv2markdown_help.txt b/docs/tsv2markdown_help.txt
new file mode 100644
index 0000000..0b2b685
--- /dev/null
+++ b/docs/tsv2markdown_help.txt
@@ -0,0 +1,40 @@
+A simple script to convert tsv (or csv) files to markdown tables using tabulate!
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py tsv2markdown
+ falmeida-py tsv2markdown [ -h|--help ]
+ falmeida-py tsv2markdown [ --tsv --csv --header ]
+
+options:
+ -h --help Show this screen.
+ --tsv= Input tsv file to print as markdown table
+ --csv= Input csv file to print as markdown table
+ --header= If file does not have a header, set a
+ custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)".
+falmeida-py: a package to the simple distribution of my custom scripts.
+
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
+ falmeida-py [ -h|--help ] [ ... ]
+
+options:
+ -h --help Show this screen
+ -v --version Show version information
+ --license Show LEGAL LICENSE information
+
+commands:
+ tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
+ splitgbk Command to split multisequence genbank files into individual files.
+ align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
+ gbk2fasta Command to convert genbank files to fasta files.
+ blasts Command to execute automatized blast commands.
+ replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
+ mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
+ bacannot2json Command to summarize main bacannot annotation results into JSON file
+
+Use: `falmeida-py -h` to get more help and see examples.
diff --git a/falmeida-py-runner.py b/falmeida-py-runner.py
new file mode 100755
index 0000000..90dbc71
--- /dev/null
+++ b/falmeida-py-runner.py
@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+"""
+This script allows a user to run fa-py without a pip/setuptools installation. Assuming all
+dependencies are installed, they can simply clone the repo and run this script.
+
+Copyright 2020 Felipe Almeida (almeidafmarques@gmail.com)
+https://github.com/fmalmeida/pythonScripts
+
+This file is part of my custom python scripts (fa-py) package, which is free: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by the Free Software Foundation,
+either version 3 of the License, or (at your option) any later version. This package is distributed
+in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+details. You should have received a copy of the GNU General Public License along with fa-py package.
+If not, see .
+"""
+
+from falmeida_py.__main__ import main
+
+
+if __name__ == '__main__':
+ main()
diff --git a/falmeida_py/__init__.py b/falmeida_py/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/falmeida_py/__main__.py b/falmeida_py/__main__.py
new file mode 100644
index 0000000..4b94bba
--- /dev/null
+++ b/falmeida_py/__main__.py
@@ -0,0 +1,249 @@
+#!/usr/bin/env python3
+license="""
+Copyright 2021 Felipe Almeida (almeidafmarques@gmail.com)
+https://github.com/fmalmeida/pythonScripts
+
+This file is part of my custom python scripts (falmeida-py) package, which is free: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by the Free Software Foundation,
+either version 3 of the License, or (at your option) any later version. This package is distributed
+in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+details. You should have received a copy of the GNU General Public License along with falmeida-py package.
+If not, see .
+"""
+
+## Def main help
+usage="""
+falmeida-py: a package to the simple distribution of my custom scripts.
+
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py [ -h|--help ] [ -v|--version ] [ --license ]
+ falmeida-py [ -h|--help ] [ ... ]
+
+options:
+ -h --help Show this screen
+ -v --version Show version information
+ --license Show LEGAL LICENSE information
+
+commands:
+ tsv2markdown Command for rapid convertion of tsv or csv to markdown tables.
+ splitgbk Command to split multisequence genbank files into individual files.
+ align2subsetgbk Command to subset genbank files based on alignments to a FASTA file.
+ gbk2fasta Command to convert genbank files to fasta files.
+ blasts Command to execute automatized blast commands.
+ replace_fasta_seq Command to replace strings in a FASTA using defitinitions from a BED file
+ mpgap2csv Command to summarize main mpgap multiqc assembly statistics into a CSV file
+ bacannot2json Command to summarize main bacannot annotation results into JSON file
+
+Use: `falmeida-py -h` to get more help and see examples.
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from docopt import docopt
+
+########################
+### Import functions ###
+########################
+from .version import *
+from .tsv2markdown import *
+from .splitgbk import *
+from .gbk2fasta import *
+from .blasts import *
+from .align2subsetgbk import *
+from .replace_fasta_seq import *
+from .bacannot2json import usage_bacannot2json,bacannot2json
+from .mpgap2csv import usage_mpgap2csv,mpgap2csv
+
+## Defining main
+def main():
+ # Parse docopt
+ __version__ = get_version()
+ arguments = docopt(usage, version=__version__, help=False, options_first=True)
+
+ ############################
+ ### tsv2markdown command ###
+ ############################
+ if arguments[''] == 'tsv2markdown':
+
+ # Parse docopt
+ args = docopt(usage_tsv2markdown, version=__version__, help=False)
+
+ # run script
+ if args['--help']:
+ print(usage_tsv2markdown.strip())
+
+ elif args['--tsv']:
+ file2mw(args['--tsv'], '\t', args['--header'])
+
+ elif args['--csv']:
+ file2mw(args['--csv'], ',', args['--header'])
+
+ else:
+ print(usage_tsv2markdown.strip())
+
+ #########################
+ ### Split gbk command ###
+ #########################
+ elif arguments[''] == 'splitgbk':
+ # Parse docopt
+ args = docopt(usage_splitgbk, version=__version__, help=False)
+
+ # Run
+ if args['--help']:
+ print(usage_splitgbk.strip())
+
+ elif args['--gbk']:
+ splitgbk(args['--gbk'], args['--outdir'])
+
+ else:
+ print(usage_splitgbk.strip())
+
+ ######################
+ ### Blast commands ###
+ ######################
+ elif arguments[''] == 'blasts':
+ # Parse docopt
+ args = docopt(usage_blasts, version=__version__, help=False)
+
+ # Run
+ if args['--help']:
+ print(usage_blasts.strip())
+
+ elif args['--query'] and args['--subject']:
+
+ ## check if task is correct
+ if args['--task'].lower() in ['blastn', 'tblastn', 'blastp', 'blastx']:
+ ## run blast
+ blast(task=args['--task'].lower(), query=args['--query'],
+ subject=args['--subject'], culling=args['--culling_limit'],
+ minid=args['--minid'], mincov=args['--mincov'], out=args['--out'],
+ threads=args['--threads'], twoway=args['--2way'])
+ ## summary
+ summary(output=args['--out'])
+ else:
+ print(f"PROBLEM!\nI could not understand the task \"{args['--task'].lower()}\", please select one of: blastn, tblastn, blastp or blastx.")
+
+ else:
+ print(usage_blasts.strip())
+
+ ######################################
+ ### Subset gbk with fasta commands ###
+ ######################################
+ elif arguments[''] == 'align2subsetgbk':
+ # Parse docopt
+ args = docopt(usage_align2subsetgbk, version=__version__, help=False)
+
+ # Run
+ if args['--help']:
+ print(usage_align2subsetgbk.strip())
+
+ elif args['--gbk'] and args['--fasta']:
+
+ # Run
+ print(f"Processing file: {args['--gbk']}!")
+ gbk2fasta(gbk=args['--gbk'])
+ blast(task='blastn', query=args['--fasta'], subject='tmp_gbk.fa',
+ culling=args['--culling_limit'], minid=args['--minid'], mincov=args['--mincov'],
+ out='out.blast', threads=1, twoway=None)
+ filtergbk(gbk=args['--gbk'], out=args['--out'], extension=int(args['--extension']))
+
+ # Clean dir
+ os.system(f"rm -rf tmp_gbk.fa out.blast")
+
+ else:
+ print(usage_align2subsetgbk.strip())
+
+ ###################################
+ ### Replace fasta seq using bed ###
+ ###################################
+ elif arguments[''] == 'replace_fasta_seq':
+ # Parse docopt
+ args = docopt(usage_replace_fasta_seq, version=__version__, help=False)
+
+ # Run
+ if args['--help']:
+ print(usage_replace_fasta_seq.strip())
+
+ elif args['--fasta'] and args['--bed']:
+
+ # Run
+ print(f"Processing file: {args['--fasta']}!")
+ replace_fasta_seq(input=args['--fasta'], bed=args['--bed'], output=args['--out'])
+ print(f"Done!")
+
+ else:
+ print(usage_replace_fasta_seq.strip())
+
+ ###########################
+ ### Convert gbk 2 fasta ###
+ ###########################
+ elif arguments[''] == 'gbk2fasta':
+ # Parse docopt
+ args = docopt(usage_gbk2fasta, version=__version__, help=False)
+
+ # run script
+ if args['--help']:
+ print(usage_gbk2fasta.strip())
+
+ elif args['--gbk']:
+ convertgbk(genbank=args['--gbk'], genes_list=args['--fofn'])
+
+ else:
+ print(usage_gbk2fasta.strip())
+
+ #############################
+ ### bacannot2json command ###
+ #############################
+ if arguments[''] == 'bacannot2json':
+
+ # Parse docopt
+ args = docopt(usage_bacannot2json, version=__version__, help=False)
+
+ # run script
+ if args['--help']:
+ print(usage_bacannot2json.strip())
+
+ elif args['--input']:
+ bacannot2json(args['--input'], args['--output'], args['--print'])
+
+ else:
+ print(usage_bacannot2json.strip())
+
+ #########################
+ ### mpgap2csv command ###
+ #########################
+ elif arguments[''] == 'mpgap2csv':
+
+ # Parse docopt
+ args = docopt(usage_mpgap2csv, version=__version__, help=False)
+
+ # run script
+ if args['--help']:
+ print(usage_mpgap2csv.strip())
+
+ elif args['--input']:
+ mpgap2csv(args['--input'], args['--output'])
+
+ else:
+ print(usage_mpgap2csv.strip())
+
+ #####################
+ ### Check license ###
+ #####################
+ elif arguments['--license']:
+ print(license.strip())
+
+ #######################################
+ ### Without commands nor parameters ###
+ #######################################
+ elif not arguments['']:
+ print(usage.strip())
+
+## Calling main
+if __name__ == '__main__':
+ main()
diff --git a/falmeida_py/align2subsetgbk.py b/falmeida_py/align2subsetgbk.py
new file mode 100644
index 0000000..29fcec8
--- /dev/null
+++ b/falmeida_py/align2subsetgbk.py
@@ -0,0 +1,80 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+########################
+### Def help message ###
+########################
+usage_align2subsetgbk = """
+A script meant to subset a genbank annotation file based on alignments against a query (Nucleotide) FASTA file
+
+---
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+Usage:
+ falmeida-py align2subsetgbk [ -h|--help ]
+ falmeida-py align2subsetgbk [ --gbk --fasta --out --minid --mincov --culling_limit --extension ]
+
+Options:
+ -h --help Show this screen.
+ -g --gbk= Gbk file for subset
+ -f --fasta= FASTA (nucl) file for querying the gbk
+ -o --out= Gbk filtered output file [Default: out.gbk].
+ --extension= Base pair length to extend the flank regions in the alignment [Default: 0].
+ --minid= Min. Identity percentage for gene annotation [Default: 80].
+ --mincov= Min. Covereage for gene annotation [Default: 80].
+ --culling_limit= Blast culling_limit for best hit only [Default: 1].
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from docopt import docopt
+from Bio import SeqIO
+import pandas as pd
+from .blasts import *
+
+##########################################
+### Function to convert gbk into fasta ###
+##########################################
+def gbk2fasta(gbk):
+ f=open("tmp_gbk.fa", "a")
+ for seq_record in SeqIO.parse(gbk, 'genbank'):
+ print(f">{seq_record.id}\n{seq_record.seq}\n", file=f)
+
+############################################
+### Function to filter gbk based on hits ###
+############################################
+def filtergbk(gbk, out, extension):
+
+ f=open(f"{out}", "w")
+ # Read blast results
+ blast_res = pd.read_csv('out.blast', sep = '\t')
+ print(blast_res)
+
+ # Get locus_tags
+ contigs = sorted(set(blast_res["sseqid"].tolist()))
+
+ # Subset
+ for contig in contigs:
+ for seq_record in SeqIO.parse(gbk, 'genbank'):
+ if str(contig) == str(seq_record.id):
+ filtered = []
+ small_df = blast_res[blast_res['sseqid'].isin([seq_record.id])]
+ for index, row in small_df.iterrows():
+ for features in seq_record.features:
+ # plus strand
+ if int(row["sstart"]) <= int(row["send"]):
+ if int(features.location.start) >= int(row["sstart"] - extension) and int(features.location.start) <= int(row["send"] + extension) and features.type != "source":
+ filtered.append(features)
+ # minus strand
+ elif int(row["sstart"]) >= int(row["send"]):
+ if int(features.location.start) >= int(row["send"] - extension) and int(features.location.start) <= int(row["sstart"] + extension) and features.type != "source":
+ filtered.append(features)
+
+ # Print results
+ seq_record.features = filtered
+ if len(seq_record.features) > 0:
+ SeqIO.write(seq_record, f, 'gb')
+ else:
+ pass
diff --git a/falmeida_py/bacannot2json.py b/falmeida_py/bacannot2json.py
new file mode 100644
index 0000000..b4a8b75
--- /dev/null
+++ b/falmeida_py/bacannot2json.py
@@ -0,0 +1,131 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+########################
+### Def help message ###
+########################
+usage_bacannot2json = """
+A script to summarize the main annotation results of fmalmeida/bacannot pipeline as a structured JSON file.
+
+---
+Copyright (C) 2022 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+Usage:
+ falmeida-py bacannot2json [ -h|--help ]
+ falmeida-py bacannot2json [ --input --output --print ]
+
+Options:
+ -h --help Show this screen.
+ -i --input= Path to bacannot results folder.
+ -o --output= JSON summary output file [Default: bacannot_summary.json].
+ -p --print Also print resolved JSON to stdout.
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from docopt import docopt
+import pandas as pd
+import json
+import simplejson
+import os
+import yaml
+from pathlib import Path
+from .utils import find_files
+from .general_stats_function import *
+from .plasmid_function import *
+from .virulence_function import *
+from .resistance_function import *
+from .mges_function import *
+
+##############################
+### fix keys in dictionary ###
+##############################
+def convert_dictkey(d):
+ ###change all keys in a dict d
+ return { str(k): convert_dictvalue(v) for k,v in d.items() }
+
+def convert_dictvalue(v):
+ ###if v is a dict do convert_dictkey() for v, else raise v
+ if isinstance(v, dict):
+ return convert_dictkey(v)
+ else:
+ return v
+
+def stringify_keys(d):
+ """Convert a dict's keys to strings if they are not."""
+ return convert_dictkey(d)
+
+###############################################
+### based on annotations figure sample name ###
+###############################################
+def get_samples(filepaths):
+ samples = []
+ for annotation in filepaths:
+ if not 'jbrowse' in str(annotation):
+ sample = annotation.split('/')[-2]
+ samples.append(sample)
+ return samples
+
+#############################
+### initialize dictionary ###
+#############################
+def dict_init(indir):
+ # main dictionary for json final output
+ bacannot_summary = {}
+
+ # detect available sample annotations
+ available_annotations = [ str(x) for x in find_files(start_dir=indir, pattern='annotation') ]
+
+ # detect available samples
+ available_samples = [ str(x) for x in get_samples(available_annotations) ]
+
+ # initiate first dictionary level
+ for sample in available_samples:
+ bacannot_summary[sample] = {}
+ bacannot_summary[sample]['sample'] = f"{sample}"
+ bacannot_summary[sample]['results_dir'] = f"{indir}/{sample}"
+
+ return bacannot_summary
+
+#######################################
+### Def main bacannot2json function ###
+#######################################
+def bacannot2json(indir, outfile, check):
+
+ # initialize
+ bacannot_dir = os.path.abspath( indir )
+ bacannot_summary = dict_init( bacannot_dir )
+
+ # check general annotation stats
+ general_stats( bacannot_summary )
+
+ # check virulence annotation stats
+ virulence_stats( bacannot_summary )
+
+ # check MGEs annotation stats
+ mges_stats( bacannot_summary )
+
+ # check plasmids annotation stats
+ plasmids_stats( bacannot_summary )
+
+ # check resistance annotation stats
+ resistance_stats( bacannot_summary )
+
+ # save results
+ final_results = simplejson.dumps(
+ stringify_keys( bacannot_summary ),
+ sort_keys=True,
+ indent=4,
+ ignore_nan=True
+ )
+ with open(outfile, 'w') as file:
+ file.write(final_results)
+
+ # keep checking
+ if check:
+ print( final_results )
+
+ # bye bye
+ print(f"==> Output generated and saved at:\n\t{outfile}")
\ No newline at end of file
diff --git a/falmeida_py/blasts.py b/falmeida_py/blasts.py
new file mode 100644
index 0000000..9fe9de4
--- /dev/null
+++ b/falmeida_py/blasts.py
@@ -0,0 +1,104 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+## Def help message
+usage_blasts = """
+A simple script to automatize the execution and filtering of blast alignments.
+
+---
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+Usage:
+ falmeida-py blasts
+ falmeida-py blasts -h|--help
+ falmeida-py blasts -v|--version
+ falmeida-py blasts ( --query --subject ) [ --task --minid --mincov --culling_limit --out --threads --2way ]
+
+Options:
+ -h --help Show this screen.
+ -v --version Show version information
+ --task= Select which task to run (blastn, blastp, tblastn or blastx) [Default: blastn].
+ --2way Sets the pipeline to filter alignments by coverage in a 2way manner.
+ Which means an alignment must cover at least n from the query and
+ subject lengths. Otherwise it just needs to cover n from query seq.
+ This method is good when comparing query genes to subject genes.
+ --query= Query fasta file.
+ --subject= Subject fasta file.
+ --minid= Min. Identity percentage for gene annotation [Default: 80]
+ --mincov= Min. Covereage for gene annotation [Default: 80]
+ --culling_limit= Blast culling_limit for best hit only [Default: 1]
+ --out= File for saving blast outputs [Default: out.blast]
+ --threads= Number of threads to be used [Default: 1]
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+import pandas as pd
+import os
+
+######################
+### BLAST FUNCTION ###
+######################
+def blast(task, query, subject, culling, minid, mincov, out, threads, twoway):
+
+ # Outfmt
+ outfmt="6 qseqid qstart qend qlen sseqid sstart send slen evalue length pident gaps gapopen bitscore"
+
+ # format header
+ os.system(f"echo \"qseqid\tqstart\tqend\tqlen\tsseqid\tsstart\tsend\tslen\tevalue\tlength\tpident\tgaps\tgapopen\tbitscore\" > {out}")
+
+ # format db
+ if task == "blastn" or task == "tblastn":
+ db_type = "nucl"
+ elif task == "blastx" or task == "blastp":
+ db_type = "prot"
+ os.system(f"makeblastdb -in {subject} -out ./FA-PY-SUBJECT-DB -dbtype {db_type} 1> /dev/null")
+
+ # run blast
+ if twoway:
+ os.system(f"{task} -query {query} -db ./FA-PY-SUBJECT-DB -outfmt \"{outfmt}\" -num_threads {threads} -culling_limit {culling} | \
+ awk -v minid={minid} -v mincov={mincov} '{{ if ($11 >= minid && (($10 - $12) / $8 * 100) >= mincov && (($10 - $12) / $4 * 100) >= mincov) {{print $0}} }}' >> {out} ")
+ else:
+ os.system(f"{task} -query {query} -db ./FA-PY-SUBJECT-DB -outfmt \"{outfmt}\" -num_threads {threads} -culling_limit {culling} | \
+ awk -v minid={minid} -v mincov={mincov} '{{ if ($11 >= minid && (($10 - $12) / $4 * 100) >= mincov) {{print $0}} }}' >> {out} ")
+
+ # clear work dir
+ os.system("rm -rf ./FA-PY-SUBJECT-DB*")
+
+########################
+### Summary function ###
+########################
+def summary(output):
+
+ # Outfmt
+ columns="QUERY\tQUERY_START\tQUERY_END\tQUERY_STRAND\t%QUERY_COV\tSUBJECT\tSUBJECT_START\tSUBJECT_END\tSUBJECT_STRAND\t%SUBJECT_COV\t%IDENTITY\tGAPS"
+
+ # Summary
+ blast = pd.read_csv(output, sep="\t")
+ print(columns)
+ for index, line in blast.iterrows():
+ # Query strand
+ if (line['qstart'] > line['qend']):
+ strand="-"
+ else:
+ strand="+"
+ # Subject strand
+ if (line['sstart'] > line['send']):
+ sstrand='-'
+ else:
+ sstrand='+'
+ # Parse headers
+ subject=line["sseqid"]
+ # Query coverage
+ qcov=round((100 * (line["length"] - line["gaps"]) / line["qlen"]), 2)
+ # Subject coverage
+ scov=round((100 * (line["length"] - line["gaps"]) / line["slen"]), 2)
+ # Identity
+ id=round(line["pident"], 2)
+ # Gaps
+ gaps=str(line["gapopen"]) + "/" + str(line["gaps"])
+
+ # Print
+ print(line["qseqid"], line["qstart"], line["qend"], strand, qcov,
+ subject, line["sstart"], line["send"], sstrand, scov, id, gaps, sep = "\t")
diff --git a/falmeida_py/gbk2fasta.py b/falmeida_py/gbk2fasta.py
new file mode 100644
index 0000000..a061da2
--- /dev/null
+++ b/falmeida_py/gbk2fasta.py
@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+## Def help message
+usage_gbk2fasta = """
+A simple script to automatize the execution and filtering of blast alignments.
+
+---
+Copyright (C) 2021 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+Usage:
+ falmeida-py gbk2fasta
+ falmeida-py gbk2fasta -h|--help
+ falmeida-py gbk2fasta -v|--version
+ falmeida-py gbk2fasta ( --gbk ) [ --out --fofn --type ]
+
+Options:
+ -h --help Show this screen.
+ -v --version Show version information
+ -g --gbk Genbank file to be converted to fasta
+ -o --out Output fasta file [Default: stdout]
+ -f --fofn File with the list of genes to be extracted. One gene per line, using the 'locus_tag' field.
+ -t --type Type of sequence to output genes: nucl or prot [Default: prot]
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from Bio import SeqIO
+
+#########################################
+### load list of genes as python list ###
+#########################################
+def load_gene_list(genes_list):
+ """
+ Loads a list of genes from a file.
+ """
+ genes = []
+ with open(genes_list, 'r') as f:
+ for line in f:
+ genes.append(line.strip())
+ return genes
+
+#################################################
+### prints a fasta from gbk biopython feature ###
+#################################################
+def print_fasta(feature, genes_list):
+ if genes_list == None:
+ print(f">{feature.qualifiers['locus_tag'][0]} {feature.qualifiers['product'][0]}")
+ print(feature.qualifiers['translation'][0])
+ else:
+ if feature.qualifiers['locus_tag'][0] in genes_list:
+ print(f">{feature.qualifiers['locus_tag'][0]} {feature.qualifiers['product'][0]}")
+ print(feature.qualifiers['translation'][0])
+
+###########################################
+### loads and converts genbank to fasta ###
+###########################################
+def convertgbk(genbank, genes_list):
+ """
+ Loads a genbank file and converts it to fasta.
+ """
+ if genes_list:
+ genes = load_gene_list(genes_list)
+ else:
+ genes = None
+ for record in SeqIO.parse(genbank, "genbank"):
+ for feature in record.features:
+ if feature.type == "CDS":
+ print_fasta(feature, genes)
\ No newline at end of file
diff --git a/falmeida_py/general_stats_function.py b/falmeida_py/general_stats_function.py
new file mode 100644
index 0000000..80e2590
--- /dev/null
+++ b/falmeida_py/general_stats_function.py
@@ -0,0 +1,48 @@
+##################################
+### Loading Necessary Packages ###
+##################################
+import pandas as pd
+import yaml
+from pathlib import Path
+
+################################
+### check general annotation ###
+################################
+def general_stats(bacannot_summary):
+
+ # iterate over available samples
+ for sample in bacannot_summary:
+
+ # load dir of samples' results
+ results_dir = bacannot_summary[sample]['results_dir']
+
+ # load annotation stats
+ general_results = yaml.safe_load(
+ Path(f"{results_dir}/annotation/{sample}.txt").read_text()
+ )
+
+ # load MLST
+ mlst_results = pd.read_csv(
+ f"{results_dir}/MLST/{sample}_mlst_analysis.txt",
+ sep='\t', header=None
+ )
+
+ # load refseq_masher
+ refseq_masher_results = pd.read_csv(
+ f"{results_dir}/refseq_masher/refseq_masher_results.txt",
+ sep='\t'
+ )
+ refseq_masher_results.sort_values(by='distance', ascending=True, inplace=True)
+
+ # save annotation stats
+ bacannot_summary[sample]['general_annotation'] = {}
+ bacannot_summary[sample]['general_annotation']['mlst'] = str(mlst_results[2].item()).replace('-', 'null')
+ bacannot_summary[sample]['general_annotation']['cds'] = general_results.get('CDS', 0)
+ bacannot_summary[sample]['general_annotation']['rrna'] = general_results.get('rRNA', 0)
+ bacannot_summary[sample]['general_annotation']['trna'] = general_results.get('tRNA', 0)
+ bacannot_summary[sample]['general_annotation']['tmrna'] = general_results.get('tmRNA', 0)
+
+ bacannot_summary[sample]['general_annotation']['closest_reference'] = {}
+ bacannot_summary[sample]['general_annotation']['closest_reference']['strain'] = refseq_masher_results.head(1)['top_taxonomy_name'].item()
+ bacannot_summary[sample]['general_annotation']['closest_reference']['distance'] = refseq_masher_results.head(1)['distance'].item()
+ bacannot_summary[sample]['general_annotation']['closest_reference']['accession'] = refseq_masher_results.head(1)['assembly_accession'].item()
\ No newline at end of file
diff --git a/falmeida_py/mges_function.py b/falmeida_py/mges_function.py
new file mode 100644
index 0000000..39014e0
--- /dev/null
+++ b/falmeida_py/mges_function.py
@@ -0,0 +1,169 @@
+##################################
+### Loading Necessary Packages ###
+##################################
+import pandas as pd
+import os
+from .utils import load_and_subset_gff
+
+####################################
+### check MGEs annotations stats ###
+####################################
+def mges_stats(bacannot_summary):
+
+ # iterate over available samples
+ for sample in bacannot_summary:
+
+ # load dir of samples' results
+ results_dir = bacannot_summary[sample]['results_dir']
+
+ # load gff_file
+ gff_file = f"{results_dir}/gffs/{sample}.gff"
+
+ # integron_finder
+ if os.path.exists(f"{results_dir}/integron_finder/{sample}_integrons.gff") and os.stat(f"{results_dir}/integron_finder/{sample}_integrons.gff").st_size > 0:
+
+ # init MGE annotation dictionary
+ if 'MGE' not in bacannot_summary[sample]:
+ bacannot_summary[sample]['MGE'] = {}
+
+ # init integron_finder annotation dictionary
+ bacannot_summary[sample]['MGE']['integron_finder'] = {}
+
+ # load integron_finder results
+ results = pd.read_csv(
+ f"{results_dir}/integron_finder/{sample}_integrons.gff",
+ sep='\t',
+ header=None,
+ names=[
+ 'chr', 'source', 'type', 'start', 'end', 'score', 'strand', 'frame', 'atts'
+ ]
+ )
+
+ # number of integron_finder annotations
+ total_number = len(results.index)
+ bacannot_summary[sample]['MGE']['integron_finder']['total'] = total_number
+
+ # per integron info
+ bacannot_summary[sample]['MGE']['integron_finder'] = {}
+ if int(results.shape[0]) > 0:
+ for seq in [ str(x) for x in results['chr'].unique() ]:
+
+ bacannot_summary[sample]['MGE']['integron_finder'][seq] = {}
+ for index, row in results[results['chr'] == seq].reset_index().iterrows():
+ id = row['atts'].split(';')[0].split('=')[-1]
+ bacannot_summary[sample]['MGE']['integron_finder'][seq][id] = {}
+ bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['id'] = id
+ bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['contig'] = row['chr']
+ bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['start'] = row['start']
+ bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['end'] = row['end']
+ bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['type'] = row['atts'].split(';')[1].split('=')[-1]
+ bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['source'] = row['source']
+ bacannot_summary[sample]['MGE']['integron_finder'][seq][id]['product'] = row['type']
+
+ # ICEberg database
+ ice_db_blastp = f"{results_dir}/ICEs/{sample}_iceberg_blastp_onGenes.summary.txt"
+ if os.path.exists(ice_db_blastp) and os.stat(ice_db_blastp).st_size > 0:
+
+ # init MGE annotation dictionary
+ if 'MGE' not in bacannot_summary[sample]:
+ bacannot_summary[sample]['MGE'] = {}
+
+ # init iceberg annotation dictionary
+ if 'ICE' not in bacannot_summary[sample]['MGE']:
+ bacannot_summary[sample]['MGE']['ICEberg'] = {}
+
+ # init iceberg blastp annotation dictionary
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'] = {}
+
+ # load integron_finder results
+ results = pd.read_csv(
+ ice_db_blastp,
+ sep='\t'
+ )
+
+ # load gff
+ gff = load_and_subset_gff(gff_file, 'source', 'ICEberg')
+
+ # number of integron_finder annotations
+ total_number = len(results.index)
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp']['total'] = total_number
+
+ # per gene info
+ if int(results.shape[0]) > 0:
+ for seq in [ str(x) for x in results['SEQUENCE'].unique() ]:
+
+ # details missing in output but available in gff
+ gff_row = gff[gff['attributes'].str.contains(seq)]
+ contig = gff_row['seq'].item()
+ start = gff_row['start'].item()
+ end = gff_row['end'].item()
+
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq] = {}
+ for index, row in results[results['SEQUENCE'] == seq].reset_index().iterrows():
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq] = {}
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['id'] = row['ICEBERG_ID']
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['contig'] = contig
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['start'] = start
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['end'] = end
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['accession'] = row['ACCESSION']
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['product'] = row['PRODUCT']
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['description'] = row['DESCRIPTION']
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_start'] = row['START']
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_end'] = row['END']
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_identity'] = row['%IDENTITY']
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['blast_coverage'] = row['%COVERAGE']
+ bacannot_summary[sample]['MGE']['ICEberg']['blastp'][seq]['strand'] = row['STRAND']
+
+ # PHAST database
+ phast_db_blastp = f"{results_dir}/prophages/phast_db/{sample}_phast_blastp_onGenes.summary.txt"
+ if os.path.exists(phast_db_blastp) and os.stat(phast_db_blastp).st_size > 0:
+
+ # init MGE annotation dictionary
+ if 'MGE' not in bacannot_summary[sample]:
+ bacannot_summary[sample]['MGE'] = {}
+
+ # init phast annotation dictionary
+ if 'ICE' not in bacannot_summary[sample]['MGE']:
+ bacannot_summary[sample]['MGE']['PHAST'] = {}
+
+ # init phast blastp annotation dictionary
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'] = {}
+
+ # load integron_finder results
+ results = pd.read_csv(
+ phast_db_blastp,
+ sep='\t'
+ )
+
+ # load gff
+ gff = load_and_subset_gff(gff_file, 'source', 'PHAST')
+
+ # number of integron_finder annotations
+ total_number = len(results.index)
+ bacannot_summary[sample]['MGE']['PHAST']['blastp']['total'] = total_number
+
+ # per gene info
+ if int(results.shape[0]) > 0:
+ for seq in [ str(x) for x in results['SEQUENCE'].unique() ]:
+
+ # details missing in output but available in gff
+ gff_row = gff[gff['attributes'].str.contains(seq)]
+ contig = gff_row['seq'].item()
+ start = gff_row['start'].item()
+ end = gff_row['end'].item()
+
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq] = {}
+ for index, row in results[results['SEQUENCE'] == seq].reset_index().iterrows():
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq] = {}
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['id'] = row['PHAST_ID']
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['contig'] = contig
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['start'] = start
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['end'] = end
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['accession'] = row['ACCESSION']
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['gene'] = row['GENE']
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['description'] = row['DESCRIPTION']
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_start'] = row['START']
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_end'] = row['END']
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_identity'] = row['%IDENTITY']
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['blast_coverage'] = row['%COVERAGE']
+ bacannot_summary[sample]['MGE']['PHAST']['blastp'][seq]['strand'] = row['STRAND']
\ No newline at end of file
diff --git a/falmeida_py/mpgap2csv.py b/falmeida_py/mpgap2csv.py
new file mode 100644
index 0000000..9a6e873
--- /dev/null
+++ b/falmeida_py/mpgap2csv.py
@@ -0,0 +1,119 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+########################
+### Def help message ###
+########################
+usage_mpgap2csv = """
+A simple to generate metadata .csv for quickly producing tables for papers. Uses statistics calculated with quast and busco, condensed in multiqc file, generated with fmalmeida/MpGAP pipeline.
+
+---
+Copyright (C) 2022 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+Usage:
+ falmeida-py mpgap2csv [ -h|--help ] [ --input --output ]
+
+Options:
+ -h --help Show this screen.
+ --input= Path to MpGAP outdir.
+ --output= File to save results (CSV). [Default: MpGAP_summary.csv]
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from docopt import docopt
+import pandas as pd
+import os
+from pathlib import Path
+import json
+from pprint import pprint
+
+###################################
+### Defifining useful functions ###
+###################################
+def find_multiqc_file(dir):
+ matches = []
+ for path in Path(dir).rglob('multiqc_data.json'):
+ matches.append(os.path.abspath(path.resolve()))
+ return matches
+
+def split_and_retrieve_desired_values(item):
+ values=str(item).split('/')
+ sample=values[-5]
+ method=values[-4]
+ del values[-5:]
+ outdir='/'.join(values)
+
+ return sample, method, outdir
+
+def parse_json(data, assembler, field, item):
+
+ return data['report_saved_raw_data'][field][assembler][item]
+
+def get_sample_and_assembly_info(files, df, quast_cols, busco_cols, base_columns):
+
+ for idx, item in enumerate(files):
+
+ sample, method, outdir = split_and_retrieve_desired_values(item)
+
+ with open(item) as json_file:
+ data = json.load(json_file)
+ assemblies = list(data['report_general_stats_data'][0].keys())
+
+ # quast desires
+ quast_selection = []
+ for index, val in enumerate(assemblies):
+ quast_selection.append( val )
+ for selection in quast_cols:
+ quast_selection.append( parse_json(
+ data, val, 'multiqc_quast', selection
+ ) )
+ quast_selection = [quast_selection[n:n+10] for n in range(0, len(quast_selection), 10)]
+
+ # busco desires
+ busco_selection = []
+ for index, val in enumerate(assemblies):
+ busco_selection.append( val )
+ for selection in busco_cols:
+ busco_selection.append( parse_json(
+ data, val, 'multiqc_busco', selection
+ ) )
+ busco_selection = [busco_selection[n:n+7] for n in range(0, len(busco_selection), 7)]
+
+ for index, val in enumerate(assemblies):
+ final = [sample, method, outdir, item, val] + quast_selection[index][1:] + busco_selection[index][1:]
+ df.loc[len(df)] = final
+ # print(final)
+
+
+
+####################
+## Defining main ###
+####################
+def mpgap2csv(indir, output):
+
+ base_columns = [ "sample", "method", "outdir", "multiqc_file", "software" ]
+ desired_quast_columns = [
+ "# contigs", "N50", "Total length",
+ "# total reads", "Properly paired (%)", "Avg. coverage depth",
+ "# predicted rRNA genes", "Complete BUSCO (%)", "Partial BUSCO (%)"
+ ]
+ desired_busco_columns = [
+ "complete_single_copy", "complete_duplicated", "fragmented",
+ "missing", "total", "lineage_dataset"
+ ]
+ multiqc_files_df = pd.DataFrame(columns = list(base_columns + desired_quast_columns + desired_busco_columns))
+
+ get_sample_and_assembly_info(
+ find_multiqc_file(indir),
+ multiqc_files_df,
+ desired_quast_columns,
+ desired_busco_columns,
+ base_columns
+ )
+
+ # save file
+ multiqc_files_df.to_csv(output, index=False)
+ print(f"=> Saved results in:\n\t{output}")
diff --git a/falmeida_py/plasmid_function.py b/falmeida_py/plasmid_function.py
new file mode 100644
index 0000000..789aa9a
--- /dev/null
+++ b/falmeida_py/plasmid_function.py
@@ -0,0 +1,133 @@
+##################################
+### Loading Necessary Packages ###
+##################################
+import pandas as pd
+import os
+
+########################################
+### check plasmids annotations stats ###
+########################################
+def plasmids_stats(bacannot_summary):
+
+ # iterate over available samples
+ for sample in bacannot_summary:
+
+ # load dir of samples' results
+ results_dir = bacannot_summary[sample]['results_dir']
+
+ # init plasmids annotation dictionary
+ bacannot_summary[sample]['plasmid'] = {}
+
+ # platon
+ if os.path.exists(f"{results_dir}/plasmids/platon/{sample}.tsv") and os.stat(f"{results_dir}/plasmids/platon/{sample}.tsv").st_size > 0:
+
+ # init platon annotation dictionary
+ bacannot_summary[sample]['plasmid']['platon'] = {}
+
+ # load platon results
+ results = pd.read_csv(
+ f"{results_dir}/plasmids/platon/{sample}.tsv",
+ sep='\t'
+ )
+
+ # number of plasmid annotations
+ total_number = len(results.index)
+ bacannot_summary[sample]['plasmid']['platon']['total'] = total_number
+
+ # per plasmid info
+ if int(results.shape[0]) > 0:
+ for seq in [x for x in results['ID'].unique()]:
+ bacannot_summary[sample]['plasmid']['platon'][seq] = {}
+ bacannot_summary[sample]['plasmid']['platon'][seq]['Length'] = results.loc[results['ID'] == seq, 'Length'].item()
+ bacannot_summary[sample]['plasmid']['platon'][seq]['ORFs'] = results.loc[results['ID'] == seq, '# ORFs'].item()
+ bacannot_summary[sample]['plasmid']['platon'][seq]['Circular'] = results.loc[results['ID'] == seq, 'Circular'].item()
+ bacannot_summary[sample]['plasmid']['platon'][seq]['AMRs'] = results.loc[results['ID'] == seq, '# AMRs'].item()
+ bacannot_summary[sample]['plasmid']['platon'][seq]['Replication'] = results.loc[results['ID'] == seq, '# Replication'].item()
+ bacannot_summary[sample]['plasmid']['platon'][seq]['Mobilization'] = results.loc[results['ID'] == seq, '# Mobilization'].item()
+ bacannot_summary[sample]['plasmid']['platon'][seq]['Conjugation'] = results.loc[results['ID'] == seq, '# Conjugation'].item()
+
+ # plasmidfinder
+ if os.path.exists(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv") and os.stat(f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv").st_size > 0:
+
+ # init platon annotation dictionary
+ bacannot_summary[sample]['plasmid']['plasmidfinder'] = {}
+
+ # load platon results
+ results = pd.read_csv(
+ f"{results_dir}/plasmids/plasmidfinder/results_tab.tsv",
+ sep='\t'
+ )
+
+ if not results.empty:
+
+ # databases
+ print( results['Database'].unique() )
+ bacannot_summary[sample]['plasmid']['plasmidfinder']['meta'] = {}
+ db_arr = results['Database'].unique()
+ bacannot_summary[sample]['plasmid']['plasmidfinder']['meta']['database'] = db_arr.tolist() if len(db_arr) > 1 else db_arr.item()
+
+ # number of plasmid annotations
+ total_number = len(results['Contig'].unique())
+ bacannot_summary[sample]['plasmid']['plasmidfinder']['total'] = total_number
+
+ # plasmid annotations contigs
+ for seq in [ str(x) for x in results['Contig'].unique() ]:
+ bacannot_summary[sample]['plasmid']['plasmidfinder'][seq] = {}
+ bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['inc_types'] = {}
+ bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['identity'] = {}
+ bacannot_summary[sample]['plasmid']['plasmidfinder'][seq]['accession'] = {}
+
+ for index, row in results.iterrows():
+ contig = str(row['Contig'])
+ bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['inc_types'] = row['Plasmid']
+ bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['identity'] = row['Identity']
+ bacannot_summary[sample]['plasmid']['plasmidfinder'][contig]['accession'] = row['Accession number']
+
+ # mob suite
+ if os.path.exists(f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt") and os.stat(f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt").st_size > 0:
+
+ # init integron_finder annotation dictionary
+ bacannot_summary[sample]['plasmid']['mob_suite'] = {}
+
+ # load integron_finder results
+ results = pd.read_csv(
+ f"{results_dir}/plasmids/mob_suite/{sample}_mobtyper_results.txt",
+ sep='\t',
+ header='infer',
+ # sample_id num_contigs size gc md5 rep_type(s) rep_type_accession(s) relaxase_type(s) relaxase_type_accession(s) mpf_type mpf_type_accession(s) orit_type(s) orit_accession(s) predicted_mobility mash_nearest_neighbor mash_neighbor_distance mash_neighbor_identification primary_cluster_id secondary_cluster_id predicted_host_range_overall_rank predicted_host_range_overall_name observed_host_range_ncbi_rank observed_host_range_ncbi_name reported_host_range_lit_rank reported_host_range_lit_name associated_pmid(s)
+ )
+
+ # number of plasmid types annotated annotations
+ # total_number = len(results.index) - 1 # always counts chromosome
+ # bacannot_summary[sample]['plasmid']['mob_suite']['total'] = total_number
+
+ # per integron info
+ bacannot_summary[sample]['plasmid']['mob_suite'] = {}
+ if int(results.shape[0]) > 0:
+ for seq in [ str(x) for x in results['sample_id'].unique() ]:
+
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq] = {}
+ for index, row in results[results['sample_id'].astype(str) == seq].reset_index().iterrows():
+ id = row['sample_id'] # they are the same for this result
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id] = {}
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['size'] = row['size']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['rep_type'] = row['rep_type(s)'].replace(',', '; ')
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['rep_type_accession'] = row['rep_type_accession(s)'].replace(',', '; ')
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['relaxase_type'] = row['relaxase_type(s)']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['relaxase_type_accession(s)'] = row['relaxase_type_accession(s)']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mpf_type'] = row['mpf_type']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mpf_type_accession'] = row['mpf_type_accession(s)']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['orit_type'] = row['orit_type(s)']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['orit_accession'] = row['orit_accession(s)']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_nearest_neighbor'] = row['mash_nearest_neighbor']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_neighbor_distance'] = row['mash_neighbor_distance']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['mash_neighbor_identification'] = row['mash_neighbor_identification']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['primary_cluster_id'] = row['primary_cluster_id']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['secondary_cluster_id'] = row['secondary_cluster_id']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['predicted_host_range_overall_rank'] = row['predicted_host_range_overall_rank']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['predicted_host_range_overall_name'] = row['predicted_host_range_overall_name']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['observed_host_range_ncbi_rank'] = row['observed_host_range_ncbi_rank']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['observed_host_range_ncbi_name'] = row['observed_host_range_ncbi_name']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['reported_host_range_lit_rank'] = row['reported_host_range_lit_rank']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['reported_host_range_lit_name'] = row['reported_host_range_lit_name']
+ bacannot_summary[sample]['plasmid']['mob_suite'][seq][id]['associated_pmid'] = row['associated_pmid(s)']
\ No newline at end of file
diff --git a/falmeida_py/replace_fasta_seq.py b/falmeida_py/replace_fasta_seq.py
new file mode 100644
index 0000000..98399e9
--- /dev/null
+++ b/falmeida_py/replace_fasta_seq.py
@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+# coding: utf-8
+
+########################
+### Def help message ###
+########################
+usage_replace_fasta_seq = """
+A script meant to replace a string in a FASTA file using defitions in a BED file (tab-separated).
+
+---
+Copyright (C) 2021 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+Usage:
+ falmeida-py replace_fasta_seq [ -h|--help ]
+ falmeida-py replace_fasta_seq [ --fasta --bed --out ]
+
+Options:
+ -h --help Show this screen.
+ -f --fasta= FASTA file to replace sequences in.
+ -o --out= Output FASTA file [Default: out.fasta].
+ -b --bed= BED file with replacement definitions.
+
+Comments:
+ The BED (start 0-based) file MUST be a 4 column file with the following format:
+ contig start end sub_seq
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from Bio import SeqIO
+
+##########################
+### load fasta as dict ###
+##########################
+def fasta_as_dict(fasta):
+ fasta_dict = {}
+ for seq_record in SeqIO.parse(fasta, "fasta"):
+ fasta_dict[seq_record.id] = seq_record
+ return fasta_dict
+
+#############################################
+### replace sequences using values in bed ###
+#############################################
+def replace_seq_in_dict(bed, dict):
+ with open(bed) as f:
+ for line in f:
+ contig, start, end, sub_seq = line.strip().split('\t')
+ dict[contig].seq = dict[contig].seq[:int(start)] + sub_seq + dict[contig].seq[int(end):]
+
+####################
+### output fasta ###
+####################
+def output_fasta(dict, out):
+ with open(out, 'w') as f:
+ for record in dict.values():
+ print(">" + record.id, file=f)
+ print(record.seq, file=f)
+
+#####################
+### main function ###
+#####################
+def replace_fasta_seq(input, output, bed):
+ fasta_dict = fasta_as_dict(input)
+ replace_seq_in_dict(bed, fasta_dict)
+ output_fasta(fasta_dict, output)
diff --git a/falmeida_py/resistance_function.py b/falmeida_py/resistance_function.py
new file mode 100644
index 0000000..7f7ff01
--- /dev/null
+++ b/falmeida_py/resistance_function.py
@@ -0,0 +1,189 @@
+##################################
+### Loading Necessary Packages ###
+##################################
+import pandas as pd
+from .utils import find_files
+import json
+import os
+import yaml
+from pathlib import Path
+from .utils import load_and_subset_gff
+from pprint import pprint
+
+##########################################
+### check resistance annotations stats ###
+##########################################
+def resistance_stats(bacannot_summary):
+
+ # iterate over available samples
+ for sample in bacannot_summary:
+
+ # load dir of samples' results
+ results_dir = bacannot_summary[sample]['results_dir']
+
+ # load gff_file
+ gff_file = f"{results_dir}/gffs/{sample}.gff"
+
+ # load annotation stats
+ if os.path.exists(f"{results_dir}/resistance"):
+
+ # init plasmids annotation dictionary
+ bacannot_summary[sample]['resistance'] = {}
+
+ ###########
+ ### rgi ###
+ ###########
+ if os.path.exists(f"{results_dir}/resistance/RGI/RGI_{sample}.txt") and os.stat(f"{results_dir}/resistance/RGI/RGI_{sample}.txt").st_size > 0:
+
+ # init rgi annotation dictionary
+ bacannot_summary[sample]['resistance']['rgi'] = {}
+
+ # load rgi results
+ results = pd.read_csv(
+ f"{results_dir}/resistance/RGI/RGI_{sample}.txt",
+ sep='\t'
+ )
+ results.drop_duplicates(inplace=True)
+
+ # load gff
+ gff = load_and_subset_gff(gff_file, 'source', 'CARD')
+
+ # number of annotations
+ total_number = len(results['ORF_ID'].unique())
+ bacannot_summary[sample]['resistance']['rgi']['total'] = total_number
+
+ # gene annotations
+ for gene in [ str(x) for x in results['ORF_ID'].unique() ]:
+
+ # init values
+ row = results.loc[results['ORF_ID'] == gene]
+ name_split_list = gene.split(' ')
+ gene = name_split_list[0]
+ name = ' '.join(name_split_list[1:])
+ bacannot_summary[sample]['resistance']['rgi'][gene] = {}
+ gff_row = gff[gff['attributes'].str.contains(f"ID={gene}")]
+ contig = gff_row['seq'].item()
+ start = gff_row['start'].item()
+ end = gff_row['end'].item()
+
+ # add values to dict
+ bacannot_summary[sample]['resistance']['rgi'][gene]['name'] = name
+ bacannot_summary[sample]['resistance']['rgi'][gene]['gene'] = row['Best_Hit_ARO'].item()
+ bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro'] = row['ARO'].item()
+ bacannot_summary[sample]['resistance']['rgi'][gene]['cut_off'] = row['Cut_Off'].item()
+ bacannot_summary[sample]['resistance']['rgi'][gene]['resistance_mechanism'] = row['Resistance Mechanism'].item()
+ bacannot_summary[sample]['resistance']['rgi'][gene]['gene_family'] = row['AMR Gene Family'].item()
+ bacannot_summary[sample]['resistance']['rgi'][gene]['subclass'] = row['Drug Class'].item()
+ bacannot_summary[sample]['resistance']['rgi'][gene]['identity'] = row['Best_Identities'].item()
+ bacannot_summary[sample]['resistance']['rgi'][gene]['accession'] = row['Model_ID'].item()
+ bacannot_summary[sample]['resistance']['rgi'][gene]['contig'] = contig
+ bacannot_summary[sample]['resistance']['rgi'][gene]['start'] = start
+ bacannot_summary[sample]['resistance']['rgi'][gene]['end'] = end
+
+
+ #####################
+ ### amrfinderplus ###
+ #####################
+ if os.path.exists(f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv") and os.stat(f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv").st_size > 0:
+
+ # init amrfinderplus annotation dictionary
+ bacannot_summary[sample]['resistance']['amrfinderplus'] = {}
+
+ # load amrfinderplus results
+ results = pd.read_csv(
+ f"{results_dir}/resistance/AMRFinderPlus/AMRFinder_resistance-only.tsv",
+ sep='\t'
+ )
+
+ # load gff
+ gff = load_and_subset_gff(gff_file, 'source', 'AMRFinderPlus')
+
+ # number of annotations
+ total_number = len(results['Protein identifier'].unique())
+ bacannot_summary[sample]['resistance']['amrfinderplus']['total'] = total_number
+
+ # gene annotations
+ for gene in [ str(x) for x in results['Protein identifier'].unique() ]:
+
+ # init values
+ row = results.loc[results['Protein identifier'] == gene]
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene] = {}
+ gene_name = row['Gene symbol'].item()
+ drug_class = row['Subclass'].item()
+ drug_type = row['Element type'].item()
+ identity = row['% Identity to reference sequence'].item()
+
+ gff_row = gff[gff['attributes'].str.contains(f"ID={gene}")]
+ contig = gff_row['seq'].item()
+ start = gff_row['start'].item()
+ end = gff_row['end'].item()
+
+ # add values to dict
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['gene'] = gene_name
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['subclass'] = drug_class
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['type'] = drug_type
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['identity'] = identity
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['contig'] = contig
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['start'] = start
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['end'] = end
+
+ #
+ # check for rgi orthologies
+ #
+ try:
+ if gene in bacannot_summary[sample]['resistance']['rgi']:
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro']
+ else:
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = None
+ except:
+ bacannot_summary[sample]['resistance']['amrfinderplus'][gene]['card_aro'] = None
+
+ #################
+ ### resfinder ###
+ #################
+ #
+ # TODO: Include genomic coordinates info
+ #
+ if os.path.exists(f"{results_dir}/resistance/resfinder/ResFinder_results_tab.txt") and os.stat(f"{results_dir}/resistance/resfinder/ResFinder_results_tab.txt").st_size > 0:
+
+ # init resfinder annotation dictionary
+ bacannot_summary[sample]['resistance']['resfinder'] = {}
+
+ # load gff
+ gff = load_and_subset_gff(gff_file, 'source', 'Resfinder')
+
+ # number of annotations
+ bacannot_summary[sample]['resistance']['resfinder']['total'] = len(gff.index)
+
+ # since resfinder output does not has locus_tag information
+ # for this module, we will be using the resolved gff from bacannot
+ for index, row in gff.iterrows():
+
+ # init attributes as dict
+ attributes = dict()
+ for keyvaluepair in row['attributes'].split(';'):
+ items = keyvaluepair.split('=')
+ key = items[0]
+ value = '='.join(items[1:])
+ attributes[key] = value
+ gene = attributes['ID']
+
+ # parse
+ bacannot_summary[sample]['resistance']['resfinder'][gene] = {}
+ bacannot_summary[sample]['resistance']['resfinder'][gene]['start'] = row['start']
+ bacannot_summary[sample]['resistance']['resfinder'][gene]['end'] = row['end']
+ # bacannot_summary[sample]['resistance']['resfinder'][gene]['Identity'] = row['Identity']
+ bacannot_summary[sample]['resistance']['resfinder'][gene]['name'] = attributes['Resfinder_gene']
+ bacannot_summary[sample]['resistance']['resfinder'][gene]['phenotype'] = attributes['Resfinder_phenotype']
+ bacannot_summary[sample]['resistance']['resfinder'][gene]['accession'] = attributes['Resfinder_reference']
+
+ #
+ # check for rgi orthologies
+ #
+ try:
+ if gene in bacannot_summary[sample]['resistance']['rgi']:
+ bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = bacannot_summary[sample]['resistance']['rgi'][gene]['card_aro']
+ else:
+ bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = None
+ except:
+ bacannot_summary[sample]['resistance']['resfinder'][gene]['card_aro'] = None
diff --git a/falmeida_py/splitgbk.py b/falmeida_py/splitgbk.py
new file mode 100644
index 0000000..71abdee
--- /dev/null
+++ b/falmeida_py/splitgbk.py
@@ -0,0 +1,38 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+## Def help message
+usage_splitgbk = """
+A very simple script to split multisequence genbank files into separate files
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py splitgbk
+ falmeida-py splitgbk [ -h|--help ]
+ falmeida-py splitgbk [ --gbk ] [ --outdir ]
+
+options:
+ -h --help Show this screen.
+ -g --gbk= Input genbank file to split into multiple individual files.
+ -o --outdir= Directory (must already exist) in which to write the splitted files [Default: ./].
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from Bio import SeqIO
+import os
+
+####################
+### GBK splitter ###
+####################
+def splitgbk(gbk, outdir):
+ # just parse the dir
+ if type(outdir) == list:
+ outdir = outdir[0]
+ # exec biopython
+ for rec in SeqIO.parse(gbk, "genbank"):
+ SeqIO.write([rec], open(os.path.basename(os.path.normpath(outdir)) + "/" + rec.id + ".gbk", "w"), "genbank")
+ # finish
+ print(f"Done!\nIndividual files have been written at: {outdir}")
diff --git a/falmeida_py/tsv2markdown.py b/falmeida_py/tsv2markdown.py
new file mode 100644
index 0000000..5b49933
--- /dev/null
+++ b/falmeida_py/tsv2markdown.py
@@ -0,0 +1,52 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+## Def help message
+usage_tsv2markdown = """
+A simple script to convert tsv (or csv) files to markdown tables using tabulate!
+Copyright (C) 2020 Felipe Marques de Almeida (almeidafmarques@gmail.com)
+License: Public Domain
+
+usage:
+ falmeida-py tsv2markdown
+ falmeida-py tsv2markdown [ -h|--help ]
+ falmeida-py tsv2markdown [ --tsv --csv --header ]
+
+options:
+ -h --help Show this screen.
+ --tsv= Input tsv file to print as markdown table
+ --csv= Input csv file to print as markdown table
+ --header= If file does not have a header, set a
+ custom header. E.g. --header "Planet,R (km),mass (x 10^29 kg)".
+"""
+
+##################################
+### Loading Necessary Packages ###
+##################################
+from docopt import docopt
+from tabulate import tabulate
+
+###########################
+### Read header as list ###
+###########################
+def header2list(header):
+ return header.split(',')
+
+###################################
+### Convert with header in file ###
+###################################
+def file2mw(filep, fsep, header):
+
+ # read data.frame
+ with open(filep) as file_in:
+ lines = []
+ for line in file_in:
+ words = line.split(fsep)
+ words_striped = [word.strip() for word in words]
+ lines.append(words_striped)
+
+ # generate tabulate
+ if header:
+ print(tabulate(lines, headers=header2list(header), tablefmt="github"))
+ else:
+ print(tabulate(lines, headers="firstrow", tablefmt="github"))
diff --git a/falmeida_py/utils.py b/falmeida_py/utils.py
new file mode 100644
index 0000000..99e7111
--- /dev/null
+++ b/falmeida_py/utils.py
@@ -0,0 +1,24 @@
+from pathlib import Path
+import pandas as pd
+
+def find_files(start_dir, pattern):
+ matches = []
+ for path in Path(start_dir).rglob(pattern):
+ matches.append(path.resolve())
+ return matches
+
+def load_and_subset_gff(file, col, pattern):
+ df = pd.read_csv(
+ file, sep='\t',
+ names=[
+ "seq", "source", "type", "start", "end",
+ "score", "strand", "frame", "attributes"
+ ]
+ )
+
+ filter = df[col].str.contains(pattern)
+
+ df = df[filter]
+ df.drop_duplicates(inplace=True)
+
+ return df
\ No newline at end of file
diff --git a/falmeida_py/version.py b/falmeida_py/version.py
new file mode 100644
index 0000000..e524e2d
--- /dev/null
+++ b/falmeida_py/version.py
@@ -0,0 +1,20 @@
+"""
+The version is stored here in a separate file so it can exist in only one place.
+https://stackoverflow.com/a/7071358/2438989
+
+Copyright 2022 Felipe Almeida (almeidafmarques@gmail.com)
+https://github.com/fmalmeida/pythonScripts
+
+This file is part of my custom python scripts (falmeida-py) package, which is free: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by the Free Software Foundation,
+either version 3 of the License, or (at your option) any later version. This package is distributed
+in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+details. You should have received a copy of the GNU General Public License along with falmeida-py package.
+If not, see .
+"""
+
+__version__ = '1.2.4'
+
+def get_version():
+ return __version__
diff --git a/falmeida_py/virulence_function.py b/falmeida_py/virulence_function.py
new file mode 100644
index 0000000..91e912d
--- /dev/null
+++ b/falmeida_py/virulence_function.py
@@ -0,0 +1,114 @@
+##################################
+### Loading Necessary Packages ###
+##################################
+import pandas as pd
+from .utils import find_files
+import json
+import os
+import yaml
+from pathlib import Path
+from .utils import load_and_subset_gff
+
+##################################
+### check virulence annotation ###
+##################################
+def virulence_stats(bacannot_summary):
+
+ # iterate over available samples
+ for sample in bacannot_summary:
+
+ # load dir of samples' results
+ results_dir = bacannot_summary[sample]['results_dir']
+
+ # load gff_file
+ gff_file = f"{results_dir}/gffs/{sample}.gff"
+
+ # load annotation stats
+ if os.path.exists(f"{results_dir}/virulence"):
+
+ # init virulence annotation dictionary
+ bacannot_summary[sample]['virulence'] = {}
+
+ # vfdb
+ if os.path.exists(f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt") and os.stat(f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt").st_size > 0:
+
+ # init VFDB annotation dictionary
+ bacannot_summary[sample]['virulence']['VFDB'] = {}
+
+ # load gff
+ gff = load_and_subset_gff(gff_file, 'source', 'VFDB')
+
+ # load vfdb results
+ results = pd.read_csv(
+ f"{results_dir}/virulence/vfdb/{sample}_vfdb_blastn_onGenes.summary.txt",
+ sep='\t'
+ )
+
+ # number of virulence genes
+ total_number_of_genes = len( results['SEQUENCE'].unique() )
+ bacannot_summary[sample]['virulence']['VFDB']['total'] = total_number_of_genes
+
+ # gene annotations
+ for gene in [ str(x) for x in results['SEQUENCE'].unique() ]:
+
+ # init values
+ bacannot_summary[sample]['virulence']['VFDB'][gene] = {}
+ row = results.loc[results['SEQUENCE'] == gene]
+ vf_name = row['PRODUCT'].item().split('_(')[0].replace("[", "")
+ vf_id = row['PRODUCT'].item().split('_(')[1].split(')')[0].replace(")", "")
+ vf_fullname = row['PRODUCT'].item().replace("[", "").replace("]", "")
+ gene_name = row['GENE'].item().replace(")", "").replace("(", "")
+ gff_row = gff[gff['attributes'].str.contains(gene)]
+ contig = gff_row['seq'].item()
+ start = gff_row['start'].item()
+ end = gff_row['end'].item()
+
+ # add to dict
+ bacannot_summary[sample]['virulence']['VFDB'][gene]['virulence_factor'] = vf_name
+ bacannot_summary[sample]['virulence']['VFDB'][gene]['product'] = vf_fullname
+ bacannot_summary[sample]['virulence']['VFDB'][gene]['id'] = vf_id
+ bacannot_summary[sample]['virulence']['VFDB'][gene]['gene'] = gene_name
+ bacannot_summary[sample]['virulence']['VFDB'][gene]['chr'] = contig
+ bacannot_summary[sample]['virulence']['VFDB'][gene]['start'] = start
+ bacannot_summary[sample]['virulence']['VFDB'][gene]['end'] = end
+
+ # victors
+ if os.path.exists(f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt") and os.stat(f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt").st_size > 0:
+
+ # init victors annotation dictionary
+ gff = bacannot_summary[sample]['virulence']['Victors'] = {}
+
+ # load victors results
+ results = pd.read_csv(
+ f"{results_dir}/virulence/victors/{sample}_victors_blastp_onGenes.summary.txt",
+ sep='\t'
+ )
+
+ # load gff
+ gff = load_and_subset_gff(gff_file, 'source', 'Victors')
+
+ # number of virulence genes
+ total_number_of_genes = len( results['SEQUENCE'].unique() )
+ bacannot_summary[sample]['virulence']['Victors']['total'] = total_number_of_genes
+
+ # gene annotations
+ for gene in [ str(x) for x in results['SEQUENCE'].unique() ]:
+
+ # init values
+ row = results.loc[results['SEQUENCE'] == gene]
+ bacannot_summary[sample]['virulence']['Victors'][gene] = {}
+ vf_id = row['VICTORS_ID'].item().replace("Victors_", "")
+ gene_name = row['GENE'].item()
+ product = row['DESCRIPTION'].item()
+ gff_row = gff[gff['attributes'].str.contains(gene)]
+ contig = gff_row['seq'].item()
+ start = gff_row['start'].item()
+ end = gff_row['end'].item()
+
+ # add values to dict
+ bacannot_summary[sample]['virulence']['Victors'][gene]['id'] = vf_id
+ bacannot_summary[sample]['virulence']['Victors'][gene]['name'] = gene_name
+ bacannot_summary[sample]['virulence']['Victors'][gene]['product'] = product
+ bacannot_summary[sample]['virulence']['Victors'][gene]['contig'] = contig
+ bacannot_summary[sample]['virulence']['Victors'][gene]['start'] = start
+ bacannot_summary[sample]['virulence']['Victors'][gene]['end'] = end
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
new file mode 100644
index 0000000..eff09bb
--- /dev/null
+++ b/requirements.txt
@@ -0,0 +1,7 @@
+docopt
+pandas
+tabulate
+biopython
+simplejson
+importlib_metadata
+pyyaml
diff --git a/rgitool_test/rgi2gff.py b/rgitool_test/rgi2gff.py
deleted file mode 100644
index 07c245b..0000000
--- a/rgitool_test/rgi2gff.py
+++ /dev/null
@@ -1,91 +0,0 @@
-#!/usr/bin/env python3
-
-'''rgi2gff.py last modified 2018-07-09
-
-rgi2gff.py -b RGI_out.txt > output.gff3
-
-RGI tabular output must be first parsed with:
-
-sed -i 's/ # /#/g' and sed -i 's/ /_/g'
-'''
-
-#
-import sys
-import argparse
-import time
-from collections import defaultdict
-#
-
-# Returns s truncated at the n'th (3rd by default) occurrence of the delimiter, d.
-def trunc_at(s, d, n=3):
- return d.join(s.split(d, n)[:n])
-
-
-def write_line(outlist, wayout):
- outline = "\t".join(outlist)
- print(outline, file=wayout)
-
-
-def main(argv, wayout):
- if not len(argv):
- argv.append("-h")
-
- parser = argparse.ArgumentParser(
- formatter_class=argparse.RawDescriptionHelpFormatter, description=__doc__)
- parser.add_argument('-f', '--file', help="RGI txt output file")
- args = parser.parse_args(argv)
-
- # counter for number of lines, and strand flips
- linecounter, writecounter = 0, 0
- plusstrand, minusstrand = 0, 0
-
- hitDictCounter = defaultdict(int)
- print("Starting RGI parsing on %s" % (args.file), time.asctime(), file=sys.stderr)
- for line in open(args.file, 'r'):
- linecounter += 1
- ORF_ID, Contig, Start, Stop, Orientation, Cut_Off, Pass_Bitscore, Best_Hit_Bitscore, \
- Best_Hit_ARO, Best_Identities, ARO, Model_type, SNPs_in_Best_Hit_ARO, Other_SNPs, \
- Drug_Class, Resistance_Mechanism, AMR_Gene_Family, Predicted_DNA, Predicted_Protein, \
- CARD_Protein_Sequence, Percentage_Length_Reference_Sequence, ID, Model_id= line.rstrip().split("\t")
-
- # Reformat Contig ID
- Contig = trunc_at(Contig, "_", n=2)
- # Reformat Drug_Classes
- Drug_Class = Drug_Class.replace(";_", "&")
- # Reformat Resistance_Mechanism
- Resistance_Mechanism = Resistance_Mechanism.replace(";_", "&")
- # Define attributes
- attributes = "Additional_database=CARD_RGI;CARD_gene_name={0};CARD_gene_family={1};CARD_ARO={2};CARD_target_drugs={3};CARD_resistance_mechanism={4}".format(
- Best_Hit_ARO, AMR_Gene_Family, ARO, Drug_Class, Resistance_Mechanism)
-
- #print("Starting base on {0}".format(Start), file=sys.stderr)
-
- # convert strings of start and end to integers for calculations
- iqend = int(Start)
- iqstart = int(Stop)
- # as start must always be less or equal to end, reverse them for opposite strand hits
- if iqstart <= iqend:
- strand = "+"
- outlist = [Contig, "CARD_RGI", "resistance", Start,
- Stop, Best_Hit_Bitscore , strand, ".", attributes]
- plusstrand += 1
- else:
- strand = "-"
- outlist = [Contig, "CARD_RGI", "resistance", Start,
- Stop, Best_Hit_Bitscore, strand, ".", attributes]
- minusstrand += 1
-
- writecounter += 1
-
- # Print results
- write_line(outlist, wayout)
-
- # Logs
- print("Parsed %d lines" % (linecounter), time.asctime(), file=sys.stderr)
- print("Found %d forward and %d reverse hits" % (
- plusstrand, minusstrand), time.asctime(), file=sys.stderr)
- print("Wrote %d matches" % (writecounter), time.asctime(), file=sys.stderr)
-
-
-if __name__ == "__main__":
- main(sys.argv[1:], sys.stdout)
diff --git a/setup.py b/setup.py
new file mode 100644
index 0000000..7b2d7ed
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+"""
+This is the falmeida-py installation script. Assuming you're in the same directory, it can be run
+like this: `python3 setup.py install`, or (probably better) like this: `pip3 install .`
+
+Copyright 2020 Felipe Almeida (almeidafmarques@gmail.com)
+https://github.com/fmalmeida/pythonScripts
+
+This file is part of my custom python scripts (falmeida-py) package, which is free: you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by the Free Software Foundation,
+either version 3 of the License, or (at your option) any later version. This package is distributed
+in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+details. You should have received a copy of the GNU General Public License along with falmeida-py package.
+If not, see .
+"""
+
+from setuptools import setup
+
+
+def readme():
+ with open('README.md') as f:
+ return f.read()
+
+
+# Get the program version from another file.
+__version__ = '0.0.0'
+exec(open('falmeida_py/version.py').read())
+
+with open('requirements.txt') as f:
+ required = f.read().splitlines()
+
+setup(
+ name='falmeida-py',
+ version=__version__,
+ description='falmeida-py: a package to the simple distribution of my custom scripts.',
+ long_description=readme(),
+ long_description_content_type='text/markdown',
+ url='https://github.com/fmalmeida/pythonScripts',
+ author='Felipe Almeida',
+ author_email='almeidafmarques@gmail.com',
+ license='GPLv3',
+ packages=['falmeida_py'],
+ install_requires=required,
+ entry_points={"console_scripts": ['falmeida-py = falmeida_py.__main__:main']},
+ include_package_data=True,
+ zip_safe=False,
+ python_requires='>=3.6'
+)