fix issue #14

Author: kepbod

CHANGELOG.md

@@ -1,3 +1,9 @@
+## 2.3.2 (2017-10-05)
+
+Improvements:
+
+* more safe way to trim the last comma of ref file, thanks @Tong-Chen (issue #14)
+
 ## 2.3.1 (2017-10-03)
 
 Bugfixes:
@@ -8,7 +14,7 @@ Bugfixes:
 
 Improvements:
 
-* reorganize inputs and outputs.
+* reorganize inputs and outputs
 * add alternative back-splicing analysis
 * support Python 3
 
@@ -96,7 +102,7 @@ Improvements:
 
 Bugfixes:
 
-* change module name from 'circ' to 'circ2' in case of conflict with CIRCexplorer (issue #1).
+* change module name from 'circ' to 'circ2' in case of conflict with CIRCexplorer (issue #1)
 
 ## 2.0.1 (2016-06-21)
 

circ2/assemble.py

@@ -76,8 +76,8 @@ def ref_filter(ref, tophat_dir, cufflinks_dir):
     with open(ref, 'r') as ref_f, open(filtered_junction_f, 'w') as out_f:
         for line in ref_f:
             chrom = line.split()[2]
-            starts = line.split()[10].split(',')[:-2]
-            ends = line.split()[9].split(',')[1:-1]
+            starts = line.split()[10].rstrip(',').split(',')[:-1]
+            ends = line.split()[9].rstrip(',').split(',')[1:]
             for s, e in zip(starts, ends):
                 junc_id = '%s\t%s\t%s' % (chrom, s, e)
                 if junc[junc_id] < 2:

circ2/denovo.py

@@ -132,9 +132,9 @@ def extract_novel_circ(denovo_dir, ref_path):
     with open(ref_path, 'r') as ref_f:
         for line in ref_f:
             chrom = line.split()[2]
-            for x in line.split()[9].split(',')[:-1]:
+            for x in line.split()[9].rstrip(',').split(','):
                 ref_left.add('\t'.join([chrom, x]))
-            for x in line.split()[10].split(',')[:-1]:
+            for x in line.split()[10].rstrip(',').split(','):
                 ref_right.add('\t'.join([chrom, x]))
     novel_out = '%s/novel_circ.txt' % denovo_dir
     annotated_out = '%s/annotated_circ.txt' % denovo_dir

circ2/helper.py

@@ -287,8 +287,8 @@ def genepred_to_bed(genepred, bed):
              start, end,
              cds_s, cds_e, n) = line.split()[:9]
             iso_id = '%s/%s' % (gene, iso)
-            starts = [int(x) for x in line.split()[9].split(',')[:-1]]
-            ends = [int(x) for x in line.split()[10].split(',')[:-1]]
+            starts = [int(x) for x in line.split()[9].rstrip(',').split(',')]
+            ends = [int(x) for x in line.split()[10].rstrip(',').split(',')]
             sizes, offsets = [], []
             for s, e in zip(starts, ends):
                 sizes.append(str(e - s))

circ2/parser.py

@@ -72,8 +72,8 @@ def parse_ref(ref_file, flag):
         for line in f:
             gene_id, iso_id, chrom, strand = line.split()[:4]
             total_id = '\t'.join(['iso', gene_id, iso_id, chrom, strand])
-            starts = [int(x) for x in line.split()[9].split(',')[:-1]]
-            ends = [int(x) for x in line.split()[10].split(',')[:-1]]
+            starts = [int(x) for x in line.split()[9].rstrip(',').split(',')]
+            ends = [int(x) for x in line.split()[10].rstrip(',').split(',')]
             start = starts[0]
             end = ends[-1]
             if flag == 1:

circ2/version.py

@@ -1 +1 @@
-__version__ = '2.3.1'
+__version__ = '2.3.2'