changeset 14:a234ed464674 draft default tip

Uploaded

--- a/fasta_extract.py	Sun Jan 10 14:57:50 2016 -0500
+++ b/fasta_extract.py	Sun Jan 10 15:01:05 2016 -0500
@@ -43,7 +43,6 @@
 
 fasta = Fasta(args.genome_file)
 
-dh = open('debug.log', 'wb')
 for (input_filename, hid) in args.inputs:
     extend_existing = args.extend_existing == 'existing'
     consider_strand = args.strand == 'yes'
@@ -54,7 +53,6 @@
                                         args.add_to_end,
                                         extend_existing,
                                         consider_strand)
-    dh.write('\n fasta_output_path: %s\n' % str(fasta_output_path))
     output = open(fasta_output_path, 'wb')
     gff_output_path = get_output_path(hid,
                                       args.subtract_from_start,
@@ -62,35 +60,28 @@
                                       extend_existing,
                                       consider_strand,
                                       orphan=True)
-    dh.write('\n gff_output_path: %s\n' % str(gff_output_path))
     orphan_writer = csv.writer(open(gff_output_path, 'wb'), delimiter='\t')
 
     for row in reader:
-        dh.write('\n row: %s\n' % str(row))
         if len(row) != 9 or row[0].startswith('#'):
             continue
-        try:
-            cname = row[0]
-            start = int(row[3])
-            end = int(row[4])
-            strand = row[6]
-            if extend_existing:
-                start -= args.subtract_from_start
-                end += args.add_to_end
-            else:
-                midpoint = (start + end) // 2
-                start = midpoint - args.subtract_from_start
-                end = midpoint + args.add_to_end
-            if 1 <= start and end <= len(fasta[cname]):
-                output.write('>%s:%s-%s_%s\n' % (cname, start, end, strand))
-                bases = fasta[cname][start-1:end]
-                if consider_strand and strand == '-':
-                    bases = reverse_complement(bases)
-                dh.write('\n bases: %s\n' % str(bases))
-                output.write('%s\n' % bases)
-            else:
-                orphan_writer.writerow(row)
-        except Exception, e:
-            stop_err(str(e))
+        cname = row[0]
+        start = int(row[3])
+        end = int(row[4])
+        strand = row[6]
+        if extend_existing:
+            start -= args.subtract_from_start
+            end += args.add_to_end
+        else:
+            midpoint = (start + end) // 2
+            start = midpoint - args.subtract_from_start
+            end = midpoint + args.add_to_end
+        if 1 <= start and end <= len(fasta[cname]):
+            output.write('>%s:%s-%s_%s\n' % (cname, start, end, strand))
+            bases = fasta[cname][start-1:end]
+            if consider_strand and strand == '-':
+                bases = reverse_complement(bases)
+            output.write('%s\n' % bases)
+        else:
+            orphan_writer.writerow(row)
     output.close()
-    dh.close()