details: http://www.bx.psu.edu/hg/galaxy/rev/5d92863c4860 changeset: 2663:5d92863c4860 user: Dan Blankenberg dan@bx.psu.edu date: Fri Sep 04 10:49:02 2009 -0400 description: removing debuging statements from annotation_profiler that were never inteded to go out
1 file(s) affected in this change:
tools/annotation_profiler/annotation_profiler_for_interval.py
diffs (71 lines):
diff -r e929a2d803e4 -r 5d92863c4860 tools/annotation_profiler/annotation_profiler_for_interval.py --- a/tools/annotation_profiler/annotation_profiler_for_interval.py Fri Sep 04 10:40:16 2009 -0400 +++ b/tools/annotation_profiler/annotation_profiler_for_interval.py Fri Sep 04 10:49:02 2009 -0400 @@ -26,8 +26,7 @@ self.filename = filename self.length = int( self.file_size / self.fmt_size / 2 ) self._cached_ranges = [ None for i in xrange( self.length ) ] - def __getitem__( self, i ): - old_i = i + def __getitem__( self, i ): if self._cached_ranges[i] is not None: return self._cached_ranges[i] if i < 0: i = self.length + i @@ -36,14 +35,8 @@ try: start = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0] end = struct.unpack( self.fmt, self.file.read( self.fmt_size ) )[0] - except Exception, e: - print 'filename', self.filename - print 'len', len( self ) - print 'fmtsize', self.fmt_size - print 'index', i - print 'old i', old_i - print 'offset', offset - raise IndexError( str( e ) ) + except Exception, e: + raise IndexError, e self._cached_ranges[i] = ( start, end ) return start, end def __len__( self ): @@ -148,25 +141,21 @@ if chrom not in self.chromosome_coverage: self.chromosome_coverage[chrom] = bx.bitset.BitSet( chrom_length )
- self.chromosome_coverage[chrom].set_range( region_start, region_length ) - try: - for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, region_start, region_end ): - if table_name not in self.table_coverage: - self.table_coverage[table_name] = 0 - self.table_chromosome_size[table_name] = {} - self.table_regions_overlaped_count[table_name] = 0 - self.interval_table_overlap_count[table_name] = 0 - self.table_chromosome_count[table_name] = {} - if chrom not in self.table_chromosome_size[table_name]: - self.table_chromosome_size[table_name][chrom] = self.coverage_reader._coverage[table_name][chrom]._total_coverage - self.table_chromosome_count[table_name][chrom] = len( self.coverage_reader._coverage[table_name][chrom]._coverage ) - self.table_coverage[table_name] += coverage - if coverage: - self.interval_table_overlap_count[table_name] += 1 - self.table_regions_overlaped_count[table_name] += regions - except Exception, e: - print "chrom:%s, start:%s, end%s:." % ( chrom, start, end ) - raise e + self.chromosome_coverage[chrom].set_range( region_start, region_length ) + for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, region_start, region_end ): + if table_name not in self.table_coverage: + self.table_coverage[table_name] = 0 + self.table_chromosome_size[table_name] = {} + self.table_regions_overlaped_count[table_name] = 0 + self.interval_table_overlap_count[table_name] = 0 + self.table_chromosome_count[table_name] = {} + if chrom not in self.table_chromosome_size[table_name]: + self.table_chromosome_size[table_name][chrom] = self.coverage_reader._coverage[table_name][chrom]._total_coverage + self.table_chromosome_count[table_name][chrom] = len( self.coverage_reader._coverage[table_name][chrom]._coverage ) + self.table_coverage[table_name] += coverage + if coverage: + self.interval_table_overlap_count[table_name] += 1 + self.table_regions_overlaped_count[table_name] += regions def iter_table_coverage( self ): def get_nr_coverage(): #returns non-redundant coverage, where user's input intervals have been collapse to resolve overlaps