Mercurial > repos > artbio > small_rna_maps
diff small_rna_maps.py @ 29:8b5695592784 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit c3d728b98db4987821feae40952d9797c97eaf5a"
| author | artbio |
|---|---|
| date | Fri, 04 Oct 2019 04:33:53 -0400 |
| parents | 14adf24603b6 |
| children | 183bf49fe77c |
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--- a/small_rna_maps.py Thu Apr 25 12:49:05 2019 -0400 +++ b/small_rna_maps.py Fri Oct 04 04:33:53 2019 -0400 @@ -243,9 +243,9 @@ map_dictionary[(chrom, pos+1, 'F')] = [] for key in map_dictionary: coverage = self.bam_object.count_coverage( - reference=key[0], + contig=key[0], start=key[1]-1, - end=key[1], + stop=key[1], quality_threshold=quality) """ Add the 4 coverage values """ coverage = [sum(x) for x in zip(*coverage)] @@ -298,7 +298,7 @@ sizeness[size] += sizedic[chrom][polarity][size] Strandbias = strandness['F'] + strandness['R'] if Strandbias: - Strandbias = strandness['F'] / float(Strandbias) + Strandbias = round(strandness['F'] / float(Strandbias), 2) else: Strandbias = 2 Mean = numpy.mean(sizeness.values()) @@ -313,10 +313,10 @@ try: line = [self.sample_name, chrom, polarity, size, sizedic[chrom][polarity][size], - Strandbias, sizeness[size]] + Strandbias, round(sizeness[size], 3)] except KeyError: line = [self.sample_name, chrom, polarity, size, 0, - Strandbias, sizeness[size]] + Strandbias, round(sizeness[size], 3)] line = [str(i) for i in line] out.write('\t'.join(line) + '\n')