Mercurial > repos > alenail > chipsequtil
diff chipsequtil/map_to_known_genes.py @ 4:0eaa8225a09a draft
Uploaded
author | alenail |
---|---|
date | Mon, 04 Apr 2016 14:52:14 -0400 |
parents | 4f66143b385a |
children | 182e829571f7 |
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--- a/chipsequtil/map_to_known_genes.py Wed Mar 30 15:22:19 2016 -0400 +++ b/chipsequtil/map_to_known_genes.py Mon Apr 04 14:52:14 2016 -0400 @@ -60,16 +60,6 @@ gene_ref = parse_gene_ref(args[0]) xref_fn = args[1] peaks_fn = args[2] - if opts.peaks_fmt == 'auto' : - path,ext = os.path.splitext(peaks_fn) - if ext.lower() == '.xls' : - opts.peaks_fmt = 'MACS' - elif ext.lower() == '.bed' : - opts.peaks_fmt = 'BED' - elif ext.lower() == '.narrowpeak' : - opts.peaks_fmt = 'BED' - else : - parser.error('Could not guess peaks file format by extension (%s), aborting'%ext) if opts.peaks_fmt == 'MACS' : peaks_reader_cls = MACSFile