Bugfix bamfilter

- added unmap flag to parsing without list
- removed progress flag

Author: Dominik R Laetsch

bloblib/BtIO.py

@@ -306,7 +306,7 @@ def print_bam(read_pair_out_fs, read_pair_type, read1, read2):
         fh.write("\t".join(read1) + "\n")
         fh.write("\t".join(read2) + "\n")
 
-def parseBamForFilter(infile, progress_flag, include_unmapped, outfile, include, exclude, gzip, do_sort, keep_sorted, sort_threads):
+def parseBamForFilter(infile, include_unmapped, outfile, include, exclude, gzip, do_sort, keep_sorted, sort_threads):
     '''
     parse BAM to extract readpairs
     '''
@@ -353,11 +353,11 @@ def parseBamForFilter(infile, progress_flag, include_unmapped, outfile, include,
             seen_reads += 2
             read2 = sam_lines[i+1].split()
             read_pair_type = "".join(sorted([sequence_to_type_dict[read1[2]], sequence_to_type_dict[read2[2]]]))
+            BtLog.progress(seen_reads, progress_unit, reads_total)
             if read_pair_type in pair_seqs_by_type:
                 #pair_seqs_by_type[read_pair_type] += get_read_pair_seqs(read1, read2)
                 pair_seqs_by_type[read_pair_type].append(get_read_pair_seqs(read1, read2))
                 pair_count_by_type[read_pair_type] += 1
-                BtLog.progress(seen_reads, progress_unit, reads_total)
         except IndexError:
             print BtLog.warn_d['11']
         #print_bam(read_pair_out_fs, read_pair_type, read1, read2) # this prints SAM files for debugging

bloblib/bamfilter.py

@@ -1,14 +1,13 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-"""usage: blobtools bamfilter  -b FILE [-p] [-i FILE] [-e FILE] [-u] [-o PREFIX]
+"""usage: blobtools bamfilter  -b FILE [-i FILE] [-e FILE] [-u] [-o PREFIX]
                                 [--sort] [--keep] [--threads INT]
                                 [-h|--help]
 
     Options:
         -h --help                   show this
         -b, --bam FILE              BAM file (sorted by name)
-        -p, --progress              Display progress [default: False]
         -i, --include FILE          List of contigs whose reads are included
                                     - writes interleaved FASTQs of pairs where at least
                                         one read maps sequences in list
@@ -42,7 +41,6 @@ def main():
     args = docopt(__doc__)
     bam_f = args['--bam']
     include_f = args['--include']
-    progress_flag = args['--progress']
     exclude_f = args['--exclude']
     out_prefix = args['--out']
     include_unmapped = args['--include_unmapped']
@@ -55,12 +53,12 @@ def main():
         print BtLog.error('43')
     elif include_f:
         sequence_list = BtIO.parseList(include_f)
-        BtIO.parseBamForFilter(bam_f, progress_flag, include_unmapped, out_f, sequence_list, None, gzip, do_sort, keep_sorted, sort_threads)
+        BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, sequence_list, None, gzip, do_sort, keep_sorted, sort_threads)
     elif exclude_f:
         sequence_list = BtIO.parseList(exclude_f)
-        BtIO.parseBamForFilter(bam_f, progress_flag, include_unmapped, out_f, None, sequence_list, gzip, do_sort, keep_sorted, sort_threads)
+        BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, None, sequence_list, gzip, do_sort, keep_sorted, sort_threads)
     else:
-        BtIO.parseBamForFilter(bam_f, progress_flag, out_f, None, None, gzip, do_sort, keep_sorted, sort_threads)
+        BtIO.parseBamForFilter(bam_f, include_unmapped, out_f, None, None, gzip, do_sort, keep_sorted, sort_threads)
 
 if __name__ == '__main__':
     main()