20. Matching GCFs to Reference BGCs in MIBiG

lsaBGC-MIBiGMapper

New in version 1.34 of the suite, we introduce lsaBGC-MIBiGMapper which assesses whether a reference BGC in MIBiG (v3.1) matches to a GCF.

By default it requires 5 genes in the reference BGC match 5 genes from a BGC belonging to the GCF.

This program further allows mapping homolog groups to specific genes in the reference BGCs from MIBiG and is incorporated into the final spreadsheets produced by lsaBGC-(Euk-)Easy and lsaBGC-AutoAnalyze workflows.

Usage:

usage: lsaBGC-MIBiGMapper.py [-h] -g GCF_LISTING [-i GCF_ID] -m ORTHOFINDER_MATRIX -o OUTPUT_DIRECTORY [-p BGC_PREDICTION_SOFTWARE] [-id IDENTITY] [-cov COVERAGE] [-sh SHARED]
                             [-pr SYNTENIC_CORRELATION_CUTOFF] [-d] [-c CPUS]

        Program: lsaBGC-MIBiGMapper.py
        Author: Rauf Salamzade
        Affiliation: Kalan Lab, UW Madison, Department of Medical Microbiology and Immunology

        This program will assess whether MIBiG BGCs can be grouped in with a single GCF as determined by lsaBGC-Cluster
        or BiG-SCAPE. 


optional arguments:
  -h, --help            show this help message and exit
  -g GCF_LISTING, --gcf_listing GCF_LISTING
                        BGC listings file for a gcf. Tab delimited: 1st column lists sample name
                        while the 2nd column is the path to a BGC prediction
                        in Genbank format.
  -i GCF_ID, --gcf_id GCF_ID
                        GCF identifier.
  -m ORTHOFINDER_MATRIX, --orthofinder_matrix ORTHOFINDER_MATRIX
                        OrthoFinder homolog by sample matrix.
  -o OUTPUT_DIRECTORY, --output_directory OUTPUT_DIRECTORY
                        Output directory.
  -p BGC_PREDICTION_SOFTWARE, --bgc_prediction_software BGC_PREDICTION_SOFTWARE
                        Software used to predict BGCs (Options: antiSMASH, DeepBGC, GECCO)
                        [Default is antiSMASH].
  -id IDENTITY, --identity IDENTITY
                        Minimal identity of MIBiG proteins to match GCF proteins to be
                        assigned same homolog group [Default is 60.0].
  -cov COVERAGE, --coverage COVERAGE
                        Minimal coverage of GCF proteins needed to assign MIBiG protein
                        to same homolog group [Default is 70.0].
  -sh SHARED, --shared SHARED
                        Minimal number of homolog groups of representative BGC found in MIBiG
                        BGC to consider potential match [Default is 5].
  -pr SYNTENIC_CORRELATION_CUTOFF, --syntenic_correlation_cutoff SYNTENIC_CORRELATION_CUTOFF
                        Minimum absolute correlation coefficient of
                        MIBiG BGC with representative BGC from GCF. Is not regarded if '--draft_mode' specified. [Default is 0.0].
  -d, --draft_mode      BGCs in GCF listing are fragmented. Will assess MIBiG
                        BGCs to all instances of GCF in sample - assuming multiple BGCs are due to assembly
                        fragmentation.
  -c CPUS, --cpus CPUS  Number of CPUs to use [Default is 1].