From a78d54c94d822dd1ceee0793ce39452511effafd Mon Sep 17 00:00:00 2001 From: jpuritz Date: Sun, 8 May 2016 12:48:09 -0400 Subject: [PATCH] Problem parsing new .loci format I'm not sure if this fix is needed for other output formats, but this worked to fix issues I was seeing in VCF outputs. --- pyrad/loci2vcf.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyrad/loci2vcf.py b/pyrad/loci2vcf.py index 4be8a93..3cd7ead 100644 --- a/pyrad/loci2vcf.py +++ b/pyrad/loci2vcf.py @@ -24,7 +24,7 @@ def make(WORK, version, outname, mindepth, names): print >>outfile, "##FORMAT=" print >>outfile, "\t".join(["#CHROM","POS","ID","REF","ALT","QUAL","FILTER","INFO ","FORMAT"]+list(names)) - loci = open(inloci).read().split("|")[:-1] + loci = open(inloci).read().split("|\n")[:-1] snps = 0 vcflist = [] for locusnumber in range(len(loci)):