Remove sample name parsing which doesn't work when directories have .… #100
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… in the name, instead just pass sample_name along to functions requiring it.
mbargull
reviewed
Dec 14, 2017
scripts/srst2.py
Outdated
| @@ -450,7 +450,7 @@ def read_pileup_data(pileup_file, size, prob_err, consensus_file = ""): | |||
| elif consensus_file.split(".")[-2] == "all_consensus_alleles": | |||
| consensus_type = "consensus" | |||
| with open(consensus_file, "a") as consensus_outfile: | |||
| consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, pileup_file.split(".")[1].split("__")[1])) | |||
| consensus_outfile.write(">{0}.{1} {2}\n".format(allele, consensus_type, sample_name) | |||
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… in the name, instead just pass sample_name along to functions requiring it.
This addresses #99