Mercurial > repos > fubar > htseq_bams_to_count_matrix
changeset 16:63eaa64904be draft
Uploaded
| author | fubar |
|---|---|
| date | Fri, 07 Jun 2013 02:59:49 -0400 |
| parents | 9b2f58a260e9 |
| children | 13f82e0a397c |
| files | htseq_bams_to_count_matrix/htseqsams2mx.py htseq_bams_to_count_matrix/htseqsams2mx.xml |
| diffstat | 2 files changed, 12 insertions(+), 11 deletions(-) [+] |
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--- a/htseq_bams_to_count_matrix/htseqsams2mx.py Fri Jun 07 02:46:09 2013 -0400 +++ b/htseq_bams_to_count_matrix/htseqsams2mx.py Fri Jun 07 02:59:49 2013 -0400 @@ -303,16 +303,17 @@ scolnames = [x.split(',')[1].replace("'",'').replace('"','') for x in samdat] assert len(samf) == len(scolnames), '##ERROR sams2mx: Count of sam/cname not consistent - %d/%d' % (len(samf),len(scolname)) for i,b in enumerate(samf): - assert os.path.isfile(b),'## Supplied input sam file "%s" not found' % b - sam_filenames.append(b) - sampName = scolnames[i] # better be unique - if sampName == "": - sampName = b # for test - sampName = sampName.replace('#','') # for R - sampName = sampName.replace('(','') # for R - sampName = sampName.replace(')','') # for R - sampName = sampName.replace(' ','_') # for R - colnames.append(sampName) + if b != 'None': + assert os.path.isfile(b),'## Supplied input sam file "%s" not found' % b + sam_filenames.append(b) + sampName = scolnames[i] # better be unique + if sampName == "": + sampName = b # for test + sampName = sampName.replace('#','') # for R + sampName = sampName.replace('(','') # for R + sampName = sampName.replace(')','') # for R + sampName = sampName.replace(' ','_') # for R + colnames.append(sampName) counts,empty,ambiguous,lowqual,notaligned,nonunique = htseqMX(gff_file, sam_filenames,colnames,opts) heads = '\t'.join(['Contig',] + colnames) res = [heads,]
--- a/htseq_bams_to_count_matrix/htseqsams2mx.xml Fri Jun 07 02:46:09 2013 -0400 +++ b/htseq_bams_to_count_matrix/htseqsams2mx.xml Fri Jun 07 02:59:49 2013 -0400 @@ -23,7 +23,7 @@ --samf "'$fourthsamf','${fourthsamf.name}'" #end if #for $s in $samfiles: - #if $s.samf.name: + #if $s.samf != None: --samf "'${s.samf}','${s.samf.name}'" #end if #end for