mixclone/preprocess/data.py, mixclone/preprocess/utils.py: chrom_idxs…

… bug fixed
uci-cbcl · Dec 4, 2015 · 7239369 · 7239369
1 parent 97dddd3
commit 7239369
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Showing 2 changed files with 6 additions and 4 deletions.
diff --git a/mixclone/preprocess/data.py b/mixclone/preprocess/data.py
@@ -53,7 +53,7 @@ def load_segments(self, normal_bam, tumor_bam, bed_file_name):
 
         sam_SQ = normal_bam.header['SQ']
         sam_chrom_format = get_chrom_format(map(lambda x:x['SN'], sam_SQ))
-        chrom_lens = get_chrom_lens(chrom_idx_list, sam_SQ)
+        chrom_lens, chrom_idxs = get_chrom_lens_idxs(chrom_idx_list, sam_SQ)
 
         bed_chroms, bed_starts, bed_ends = BEDParser(bed_file_name)
         bed_chrom_format = get_chrom_format(bed_chroms)
@@ -69,7 +69,7 @@ def load_segments(self, normal_bam, tumor_bam, bed_file_name):
                 sys.stdout.flush()
                 continue
 
-            chrom_lst_idx = chrom_idx_list.index(chrom_idx)
+            chrom_lst_idx = chrom_idxs.index(chrom_idx)
 
             if bed_starts[i] < chrom_start or bed_ends[i] > chrom_lens[chrom_lst_idx]:
                 print 'Out of range chromsome {0}, segment {1} excluded...'.format(bed_chroms[i], seg_name)

diff --git a/mixclone/preprocess/utils.py b/mixclone/preprocess/utils.py
@@ -84,17 +84,19 @@ def get_chrom_format(chroms):
     else:
         return format
 
-def get_chrom_lens(chrom_idx_list, sam_SQ):
+def get_chrom_lens_idxs(chrom_idx_list, sam_SQ):
     chrom_lens = []
+    chrom_idxs = []
     for i in range(0, len(chrom_idx_list)):
         chrom_idx = chrom_idx_list[i]
 
         for j in range(0, len(sam_SQ)):
             if chrom_idx == chrom_name_to_idx(sam_SQ[j]['SN']):
                 chrom_lens.append(int(sam_SQ[j]['LN']))
+                chrom_idxs.append(chrom_idx)
                 break
 
-    return chrom_lens
+    return (chrom_lens, chrom_idxs)
 
 def get_segment_name(chrom_name, start, end):