genomicepidemiology / ARGprofiler

A pipeline for for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets
Apache License 2.0
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Improve regex for finding local sequencing data #9

Open hmmartiny opened 4 days ago

hmmartiny commented 4 days ago

ARGprofiler is not capable of capturing different naming schemes for paired end read files.

Current regex is:

p_id = re.compile(r'.+\/(((\w+)_\d)|(\w+))\..+\.gz')

For example, can't capture these files: billede