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removing debuging statements from annotation_profiler that were never inteded to go out

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This commit is contained in:
Daniel Blankenberg
2009-09-04 10:49:02 -04:00
parent 87eebd3206
commit 6de4ac1c27
1 changed files with 18 additions and 29 deletions
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tools/annotation_profiler/annotation_profiler_for_interval.py
+18 -29
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@@ -26,8 +26,7 @@ class CachedRangesInFile:
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 @@ class CachedRangesInFile:
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 @@ class TableCoverageSummary:
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