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Daniel Blankenberg
2008-10-30 14:48:01 -04:00
parent b9960cf09d aeaf3c8978
commit 1de07ed5c1
1 changed files with 29 additions and 6 deletions
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tools/annotation_profiler/annotation_profiler_for_interval.py
+29 -6
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@@ -121,14 +121,27 @@ class TableCoverageSummary:
self.table_chromosome_size = {} #dict of dict of table:chrom containing total coverage of table for a chrom
self.table_chromosome_count = {} #dict of dict of table:chrom containing total number of coverage ranges of table for a chrom
self.table_regions_overlaped_count = {} #total number of table regions overlaping user's input intervals (non unique)
self.interval_table_overlap_count = {} #total number of user input intervals which overlap table
self.interval_table_overlap_count = {} #total number of user input intervals which overlap table
self.region_size_errors = {} #dictionary of lists of invalid ranges by chromosome
def add_region( self, chrom, start, end ):
self.total_interval_size += ( end - start )
chrom_length = self.chrom_lengths.get( chrom )
region_start = min( start, chrom_length )
region_end = min( end, chrom_length )
region_length = region_end - region_start
if region_length < 1 or region_start != start or region_end != end:
if chrom not in self.region_size_errors:
self.region_size_errors[chrom] = []
self.region_size_errors[chrom].append( ( start, end ) )
if region_length < 1: return
self.total_interval_size += region_length
self.total_interval_count += 1
if chrom not in self.chromosome_coverage:
self.chromosome_coverage[chrom] = bx.bitset.BitSet( self.chrom_lengths.get( chrom ) )
self.chromosome_coverage[chrom].set_range( start, end - start )
for table_name, coverage, regions in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, start, end ):
self.chromosome_coverage[chrom] = bx.bitset.BitSet( chrom_length )
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] = {}
@@ -213,7 +226,17 @@ def profile_summary( interval_filename, chrom_col, start_col, end_col, out_filen
if keep_empty or total_coverage:
#only output tables that have atleast 1 base covered unless empty are requested
out.write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( table_name, table_chromosome_size, table_chromosome_count, table_region_coverage, table_region_count, total_interval_count, total_interval_size, total_coverage, table_regions_overlaped_count, interval_region_overlap_count, nr_interval_count, nr_interval_size, nr_coverage, nr_table_regions_overlaped_count, nr_interval_table_overlap_count ) )
out.close()
out.close()
#report chrom size errors as needed:
if table_coverage_summary.region_size_errors:
print "Regions provided extended beyond known chromosome lengths, and have been truncated as necessary, for the following intervals:"
for chrom, regions in table_coverage_summary.region_size_errors.items():
if len( regions ) > 3:
extra_region_info = ", ... "
else:
extra_region_info = ""
print "%s has max length of %s, exceeded by %s%s." % ( chrom, chrom_lengths.get( chrom ), ", ".join( map( str, regions[:3] ) ), extra_region_info )
class ChromosomeLengths:
def __init__( self, filename ):