Mercurial > repos > fubar > htseq_bams_to_count_matrix
comparison htseqsams2mx.py @ 50:0edc994d4021 draft
Uploaded
| author | iuc |
|---|---|
| date | Wed, 18 Feb 2015 11:37:05 -0500 |
| parents | 390cb852aae7 |
| children |
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| 49:c57e63d1a9d2 | 50:0edc994d4021 |
|---|---|
| 128 colname = colnames[sami] | 128 colname = colnames[sami] |
| 129 isbam = sam_exts[sami] == 'bam' | 129 isbam = sam_exts[sami] == 'bam' |
| 130 hasbai = sam_bais[sami] > '' | 130 hasbai = sam_bais[sami] > '' |
| 131 if hasbai: | 131 if hasbai: |
| 132 tempname = os.path.splitext(os.path.basename(sam_filename))[0] | 132 tempname = os.path.splitext(os.path.basename(sam_filename))[0] |
| 133 tempbam = '%s.bam' % tempname | 133 tempbam = '%s_TEMP.bam' % tempname |
| 134 tempbai = '%s.bai' % tempname | 134 tempbai = '%s_TEMP.bai' % tempname |
| 135 os.link(sam_filename,tempbam) | 135 os.link(sam_filename,tempbam) |
| 136 os.link(sam_bais[sami],tempbai) | 136 os.link(sam_bais[sami],tempbai) |
| 137 try: | 137 try: |
| 138 if isbam: | 138 if isbam: |
| 139 if hasbai: | 139 if hasbai: |