autorun: A Python repository from adamkoziol

antismash-parse

Introduction

Parses results from antiSMASH. Hits are often annotated vaguely. This script performs remote blastp analyses, and associates ORFs with the original strains, and descriptions extracted from the BLAST results

Installation

git clone https://github.com/adamkoziol/antismash-parse.git cd antismash-parse python3 setup.py install

Requirements

Unix-like environment (tested in Ubuntu)
biosynML.xml file created by antiSMASH
list of clusters/ORFs of interest. This is created by running the following command in ' your antiSMASH_run folder: find -name "*_gene_info.txt" -exec grep "ctg*" {} \; | cut -f1 | uniq > contigs.txt
A folder containing all the GenBank files (.gbk) except *...final.gbk from the antiSMASH_run folder

Arguments

path: contains file of contigs
-f: name of file of contigs
-c: name and path of folder containing .gbk files

Running

Example command to run the script

parseresults.py <PATH> -f contigs.txt -c <PATH/TO/CLUSTERS

Usage

usage: parseresults.py [-h] [-f FILE] -c CLUSTERPATH path

Parses anti-SMASH output file biosyn.xml to extract protein sequencesof genes
of interest

positional arguments:
  path                  Specify input directory

optional arguments:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  Name of file of contig numbers. This is created by
                        running the following command in your antiSMASH_run
                        folder: find -name "*_gene_info.txt" -exec grep "ctg*"
                        {} \; | cut -f1 | uniq > contigs.txt
  -c CLUSTERPATH, --clusterpath CLUSTERPATH
                        Path to .gbk cluster files created by antiSMASH.
                        Required to associate renamed contigs with original
                        files

adamkoziol/autorun