Mercurial > repos > alenail > chipsequtil
comparison chipsequtil/map_to_known_genes.py @ 4:0eaa8225a09a draft
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author | alenail |
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date | Mon, 04 Apr 2016 14:52:14 -0400 |
parents | 4f66143b385a |
children | 182e829571f7 |
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3:7a910b2c72ff | 4:0eaa8225a09a |
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58 parser.error('Must provide three filename arguments') | 58 parser.error('Must provide three filename arguments') |
59 | 59 |
60 gene_ref = parse_gene_ref(args[0]) | 60 gene_ref = parse_gene_ref(args[0]) |
61 xref_fn = args[1] | 61 xref_fn = args[1] |
62 peaks_fn = args[2] | 62 peaks_fn = args[2] |
63 if opts.peaks_fmt == 'auto' : | |
64 path,ext = os.path.splitext(peaks_fn) | |
65 if ext.lower() == '.xls' : | |
66 opts.peaks_fmt = 'MACS' | |
67 elif ext.lower() == '.bed' : | |
68 opts.peaks_fmt = 'BED' | |
69 elif ext.lower() == '.narrowpeak' : | |
70 opts.peaks_fmt = 'BED' | |
71 else : | |
72 parser.error('Could not guess peaks file format by extension (%s), aborting'%ext) | |
73 | 63 |
74 if opts.peaks_fmt == 'MACS' : | 64 if opts.peaks_fmt == 'MACS' : |
75 peaks_reader_cls = MACSFile | 65 peaks_reader_cls = MACSFile |
76 chr_field, start_field, end_field = 'chr', 'start', 'end' | 66 chr_field, start_field, end_field = 'chr', 'start', 'end' |
77 elif opts.peaks_fmt == 'BED' : | 67 elif opts.peaks_fmt == 'BED' : |