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Started code for Spoligo/MIRU information retrieval for isolates with certain mutations

Sarah Ramirez-Busby requested to merge GWAS_visualization into master

Replaced gzip, added pysam, updated args Using pysam instead of gzip Fixed args to take in a mutation file from vep-count.py Started code that will try to find isolates with the given mutation(s)

Checked out vep-count.py version from master

Added stdin and stdout functionality

Separate pattern dicts, output

Created separate spoligo and miru dictionaries for separate analyses Checked for minimal output flag for output: if flagged, prints number of patterns; otherwise, it prints unique patterns with corresponding isolates

Removed requirement of input file

Renamed GWA_analyze to gwa-check-clonality

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