fix bugs

Author: xingma

CHANGELOG.md

@@ -1,3 +1,10 @@
+## 2.2.7 (2017-07-20)
+
+Bugfixes:
+
+* fix a display error in assemble step
+* fix a bug with "--low-confidence" option in annotate step
+
 ## 2.2.6 (2016-09-25)
 
 Bugfixes:

circ2/annotate.py

@@ -120,8 +120,9 @@ def annotate_fusion(ref_f, out_dir, secondary_flag=0, denovo_flag=0):
                                 left = secondary_exon['left'][gene]
                                 right = secondary_exon['right'][gene]
                                 g, s = gene.split(':')
-                                fus_loc += '\t0\t%s' % s
-                                outf.write('%s\t%s:%s\t%s:%s\n' % (fus_loc, g,
+                                # for avoid dup, use fus_loc_new
+                                fus_loc_new = fus_loc + '\t0\t%s' % s 
+                                outf.write('%s\t%s:%s\t%s:%s\n' % (fus_loc_new, g,
                                                                    left, g,
                                                                    right))
     print('Annotated %d fusion junctions!' % len(total))

circ2/assemble.py

@@ -149,22 +149,23 @@ def convert_assembly_gtf(out_dir, cufflinks_dir, ref, bb, chrom_size):
             symbol = gene_symbol[iso] if iso in gene_symbol else iso
             ref_f.write(symbol + '\t' + line)
     # convert to bigbed if needed
-    if bb and which('bedToBigBed') is not None:
-        print('Convert to BigBed file...')
-        if not chrom_size:  # no chrom size file, search it in tophat folder
-            chrom_size = '%s/tophat/chrom.size' % out_dir
-            if not os.path.isfile(chrom_size):
-                sys.exit('Please offer the path of chrom.size!')
-        bed_path = '%s/transcripts_ref.bed' % cufflinks_dir
-        genepred_to_bed(ref_path, bed_path)
-        sorted_bed_path = '%s/transcripts_ref_sorted.bed' % cufflinks_dir
-        bed = pybedtools.BedTool(bed_path)
-        bed = bed.sort()
-        bed.saveas(sorted_bed_path)
-        bb_path = '%s/transcripts_ref_sorted.bb' % cufflinks_dir
-        return_code = os.system('bedToBigBed -type=bed12 %s %s %s' %
-                                (sorted_bed_path, chrom_size, bb_path)) >> 8
-        if return_code:
-            sys.exit('Error: cannot convert bed to BigBed!')
-    else:
-        print('Could not find bedToBigBed, so skip this step!')
+    if bb:
+        if which('bedToBigBed') is not None:
+            print('Convert to BigBed file...')
+            if not chrom_size:  # no chrom size file, search it in tophat folder
+                chrom_size = '%s/tophat/chrom.size' % out_dir
+                if not os.path.isfile(chrom_size):
+                    sys.exit('Please offer the path of chrom.size!')
+            bed_path = '%s/transcripts_ref.bed' % cufflinks_dir
+            genepred_to_bed(ref_path, bed_path)
+            sorted_bed_path = '%s/transcripts_ref_sorted.bed' % cufflinks_dir
+            bed = pybedtools.BedTool(bed_path)
+            bed = bed.sort()
+            bed.saveas(sorted_bed_path)
+            bb_path = '%s/transcripts_ref_sorted.bb' % cufflinks_dir
+            return_code = os.system('bedToBigBed -type=bed12 %s %s %s' %
+                                    (sorted_bed_path, chrom_size, bb_path)) >> 8
+            if return_code:
+                sys.exit('Error: cannot convert bed to BigBed!')
+        else:
+            print('Could not find bedToBigBed, so skip this step!')

circ2/version.py

@@ -1 +1 @@
-__version__ = '2.2.6'
+__version__ = '2.2.7'