I have modified the Bowtie mapper class because the index for bowtie2… #361
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… was not being set and was picking up the bowtie index dir
sebastian-luna-valero
requested changes
Oct 26, 2017
CGATPipelines/PipelineMapping.py
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| @@ -3044,12 +3044,21 @@ def mapper(self, infiles, outfile): | |||
| nfiles -= 2 | |||
| else: | |||
| raise ValueError("unexpected number of files") | |||
| index_prefix = "%(bowtie_index_dir)s/%(genome)s_cs" | |||
| if exexutable == "bowtie": | |||
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should this be executable instead?
CGATPipelines/PipelineMapping.py
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| elif self.datatype == "fasta": | ||
| data_options.append("-f") | ||
| index_prefix = "%(bowtie_index_dir)s/%(genome)s" | ||
| if exexutable == "bowtie": |
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should this be executable instead?
CGATPipelines/PipelineMapping.py
Outdated
| else: | ||
| index_prefix = "%(bowtie_index_dir)s/%(genome)s" | ||
| if exexutable == "bowtie": |
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should this be executable instead?
CGATPipelines/PipelineMapping.py
Outdated
| index_prefix = "%(bowtie_index_dir)s/%(genome)s_cs" | ||
| if exexutable == "bowtie": | ||
| index_prefix = "%(bowtie_index_dir)s/%(genome)s_cs" | ||
| else: |
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I would even do elif executable = "bowtie2" and raise an exception in the else, as a sanity check
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Yes I agree with you. I will make the changes.
|
@sebastian-luna-valero I have made the changes you suggest. Thanks |
bug fix for ValueError
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@sebastian-luna-valero Done, many thanks |
sebastian-luna-valero
approved these changes
Oct 26, 2017
|
Thanks @Acribbs |
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… was not being set and was picking up the bowtie index dir