Mercurial > repos > alenail > chipsequtil

diff chipsequtil/map_to_known_genes.py @ 4:0eaa8225a09a draft

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Uploaded
author alenail
date Mon, 04 Apr 2016 14:52:14 -0400
parents 4f66143b385a
children 182e829571f7
line wrap: on
line diff
--- 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