Mercurial > repos > jackcurragh > ribogalaxy_bowtie_transcriptome
diff bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py @ 8:f6ef1c85b045 draft
Uploaded
| author | jackcurragh |
|---|---|
| date | Fri, 13 May 2022 09:53:29 +0000 |
| parents | 14fb4b4872e3 |
| children |
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--- a/bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py Fri Apr 22 11:08:21 2022 +0000 +++ b/bowtie_transcriptome_wrapper/bowtie_transcriptome_wrapper.py Fri May 13 09:53:29 2022 +0000 @@ -412,9 +412,13 @@ try: # prepare actual mapping commands if options.paired == 'paired': - cmd2 = 'bowtie %s %s -1 %s -2 %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output ) + # cmd2 = 'bowtie %s %s -1 %s -2 %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output, options.output ) + cmd2 = 'bowtie %s %s -1 %s -2 %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.input2, options.output ) + else: - cmd2 = 'bowtie %s %s %s > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output ) + # cmd2 = 'bowtie %s %s %s > %s | samtools view -b -S > %s' % ( aligning_cmds, ref_file_name, options.input1, options.output, options.output ) + cmd2 = 'bowtie %s %s %s > %s ' % ( aligning_cmds, ref_file_name, options.input1, options.output ) + # align tmp = tempfile.NamedTemporaryFile( dir=tmp_index_dir ).name with open(tmp, 'w') as tmp_stderr: