Store the BED file path, it seems more important that the BIM file
authorDimitri Papadopoulos <dimitri.papadopoulos@cea.fr>
Fri, 12 Jul 2013 17:02:26 +0200
changeset 295 6a88c772d7cd
parent 294 2a9b2a5acf8e
child 296 cf995b067f04
Store the BED file path, it seems more important that the BIM file
importers/localizer.py
--- a/importers/localizer.py	Fri Jul 12 16:47:39 2013 +0200
+++ b/importers/localizer.py	Fri Jul 12 17:02:26 2013 +0200
@@ -282,6 +282,7 @@
     """Import a genomic measures"""
     g_measures = {}
     # path to BED / BIM / FAM files
+    bed_path = os.path.join(measure_path, genetics_basename + '.bed')
     bim_path = os.path.join(measure_path, genetics_basename + '.bim')
     fam_path = os.path.join(measure_path, genetics_basename + '.fam')
     # read FAM file as CSV file
@@ -294,7 +295,7 @@
         genomic_measure['identifier'] = u'genomic_measure_%s' % subject_id
         genomic_measure['type'] = u'SNP'
         genomic_measure['format'] = u'plink'
-        genomic_measure['filepath'] = unicode(bim_path)
+        genomic_measure['filepath'] = unicode(bed_path)
         genomic_measure['chip_serialnum'] = None
         genomic_measure['completed'] = True
         genomic_measure['valid'] = True