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thomasvangurp / epiGBS

Code for working with epiGBS data
MIT License
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demultiplex.py put_output error #23

Open MagnificaScience opened 5 years ago

MagnificaScience commented 5 years ago

Hello Thomas,

There appear to be 3 bugs in put_output within demultiplex.py Line 656

seq1_name = '%(code)s_%(Flowcell)s_s_%(lane)s_fastq.txt' % \
            ({'code': 'R1samplecode123', 'Flowcell': Flowcell, 'lane': Lane})

Should be 

seq1_name = '%(code)s_%(Flowcell)s_s_%(lane)s_fastq.txt' % \
            ({'code': 'R1_%s' % opts.output.split('/')[-2], 'Flowcell': Flowcell, 'lane': Lane})

With the a similar change required on line 658.

Line 660 is if not os.exists(os.path.join(dir_in, seq1_name)): which does not work, but this does: if not os.path.exists(os.path.join(dir_in, seq1_name)):

With these changes made, the output for --match1 and --match2 end up with the right filename in the right place.

Thanks, Jason