Installation
git clone https://github.com/flashton2003/stx_subtyping
Requirements
Tested with Biopython v1.6.3
Test with pysam v0.6
Tested with bwa v0.7.5
Need to have bwa installed and available in your PATH (i.e. when you type bwa from any location, it runs bwa)
Tested with python v2.7.6 Tested with Mac OS X 10.9
conda create -n stx_subtyping python=2.7 bwa biopython pysam samtools=1.1
Usage
python /path/to/script/stx_subtyping.py -h python /path/to/script/stx_subtyping.py dual_stx_subtyping -h
python /path/to/script/stx_subtyping.py dual_stx_subtyping /path/to/fastq1.fastq /path/to/fastq2.fastq /path/to/contigs.fa /path/to/whereyouwanttheoutput
There are 3 running options. The best approach is dual_stx_subtyping, but if only fastqs or fastas are available, the other options can be used.
dual_stx_subtyping - Takes a pair of fastqs and a set of contigs for a strain, outputs info into output_dir
assblast_only - Use this when you only have contigs
mapsnp_only - Use this when you only have fastqs, no assemblies
If in doubt, try -h