Small Python 3 scripts to help with fungal biosynthetic gene cluster mining.
Use this script to easily rename all the 'region' GenBank files from the fungiSMASH results. This is specially important for results with generic names (e.g. 'scaffold'), if using tools like BiG-SCAPE.
usage: rename_regions.py [-h] -i INPUTFOLDER -s STRING
optional arguments:
-h, --help show this help message and exit
-i INPUTFOLDER, --inputfolder INPUTFOLDER
Path to fungiSMASH results folder
-s STRING, --string STRING
All found .gbk files will be renamed
'[string].region[XXX].gbk'
Note that this script will write consecutive region numbers (instead of fungiSMASH's default, which uses the scaffold number).
Use this script to copy GenBank files according to a taxonomical filter. It depends on Biopython.
usage: filtercopy_genbank.py [-h] -i INPUT -o OUTPUTFOLDER -t TAXONOMY_FILTER [--include INCLUDE]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input. Either a GenBank file or a folder with fungiSMASH results
-o OUTPUTFOLDER, --outputfolder OUTPUTFOLDER
Output folder where GenBank file(s) will be copied to
-t TAXONOMY_FILTER, --taxonomy_filter TAXONOMY_FILTER
Filter extraction using taxonomy within the GenBank file(s) (if annotated)
--include INCLUDE Optional list of strings used to filter GenBank files to be analyzed. Default: 'region', 'BGC'
For this filtering to work, original GenBank files must be properly annotated, e.g.:
LOCUS BGC0000003 37168 bp DNA linear PLN 03-MAY-2005
DEFINITION Alternaria alternata AF-toxin biosynthesis gene cluster (Aft9-1,
Aft10-1, Aft11-1, Aft12-1, AftR-2, Aft3-2), complete cds.
ACCESSION BGC0000003
VERSION BGC0000003.1
KEYWORDS .
SOURCE Alternaria alternata
ORGANISM Alternaria alternata
Eukaryota; Fungi; Dikarya; Ascomycota; Pezizomycotina;
Dothideomycetes; Pleosporomycetidae; Pleosporales; Pleosporineae;
Pleosporaceae; Alternaria; Alternaria alternata group.
...
Use this script to extract the amino acid sequences corresponding to genes marked by fungiSMASH 5 as 'biosynthetic'. It depends on Biopython.
usage: extract_sequences_core_enzymes.py [-h] -i INPUT -n NAME [-b] [--include INCLUDE] [-t TAXONOMY_FILTER] [-d DOMAIN]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Input. Either a GenBank file or a folder with fungiSMASH results
-n NAME, --name NAME Name of fasta file.
-b, --biosynthetic If activated, only extract proteins flagged fungiSMASH as 'biosynthetic'
--include INCLUDE Optional list of strings used to filter GenBank files to be analyzed
-t TAXONOMY_FILTER, --taxonomy_filter TAXONOMY_FILTER
Filter extraction using taxonomy within the GenBank file(s) (if annotated)
-d DOMAIN, --domain DOMAIN
Extract domain sub-sequences from core biosynthetic proteins identified by antiSMASH. Valid arguments: KS, AT, A
The headers will have the format [GenBank base name]~L[Locus number]+CDS[CDS number] BiosyntheticType:[annotated fungiSMASH type] name:[name if annotated] gene:[gene ID if annotated] protein:[protein ID if anntoatedl]. If extracting a particular domain subsequence, additional information will be added. For example:
>BGC0000003.1~L0+CDS1@0-339_PKS_KS(Iterative-KS) BiosyntheticType:T1PKS gene:AFT9-1 protein:BAD97694.1
MDPQQRLLLETTYEALENAGIPQANTNGSNTSVHVAMFTRDYDRNVYKDTVGIPKYQVTGTGEAIMSNRISHIFNLHGPS
MTIDTGCSGAMTAVSQACMSLRSGDCDIALAGAVNLIMSPDHHISMSNLHMLNAEGKSYAFDSRGAGYGRGEGVATIVMK
RLDDAVRCHDPIRAVILDAVINQDGYTAGITLPSSEAQAQLERKALNRVGLKPQEVAYIEAHGTGTAAGDAAELDALSSV
FCVDRDLPLYVGSVKSNIGHLEAASGMAALIKATLMLENEAIPPSINFSRPKENLRIDERNIKIPTALQPWPKGASARIC
VNSFGYGGTNAHAILERAP
Use this script to launch instances of fungiSMASH on a folder with GenBank files. Parameters have already been set in antismash5_parameters.tsv, which can be customized. Tested with antiSMASH 5.1.2 installed through conda.
usage: antiSMASH_on_GenBank.py [-h] -i INPUTFOLDER -r RESULTS -o OUTPUTFOLDER
[-p PROCESSES] [-c CPUS]
optional arguments:
-h, --help show this help message and exit
-i INPUTFOLDER, --inputfolder INPUTFOLDER
Place with files
-r RESULTS, --results RESULTS
Base output folder for antiSMASH intermediate results
-o OUTPUTFOLDER, --outputfolder OUTPUTFOLDER
Base output directory used for antiSMASH _final_
GenBank files
-p PROCESSES, --processes PROCESSES
Number of simultaneous antiSMASH processes. Default: 2
-c CPUS, --cpus CPUS CPUs used for each antiSMASH run. Default: 2
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