annotation_profiler: annotation_profiler_for

comparison annotation_profiler_for_interval.py @ 0:3b33da018e74 draft default tip

Imported from capsule None

author	devteam
date	Mon, 19 May 2014 12:33:42 -0400
parents
children

comparison

equal deleted inserted replaced

--1:000000000000
+:3b33da018e74
+#!/usr/bin/env python
+#Dan Blankenberg
+#For a set of intervals, this tool returns the same set of intervals
+#with 2 additional fields: the name of a Table/Feature and the number of
+#bases covered. The original intervals are repeated for each Table/Feature.
+import sys, struct, optparse, os, random
+import bx.intervals.io
+import bx.bitset
+try:
+import psyco
+psyco.full()
+except:
+pass
+assert sys.version_info[:2] >= ( 2, 4 )
+class CachedRangesInFile:
+DEFAULT_STRUCT_FORMAT = '<I'
+def __init__( self, filename, profiler_info ):
+self.file_size = os.stat( filename ).st_size
+self.file = open( filename, 'rb' )
+self.filename = filename
+self.fmt = profiler_info.get( 'profiler_struct_format', self.DEFAULT_STRUCT_FORMAT )
+self.fmt_size = int( profiler_info.get( 'profiler_struct_size', struct.calcsize( self.fmt ) ) )
+self.length = int( self.file_size / self.fmt_size / 2 )
+self._cached_ranges = [ None for i in xrange( self.length ) ]
+def __getitem__( self, i ):
+if self._cached_ranges[i] is not None:
+return self._cached_ranges[i]
+if i < 0: i = self.length + i
+offset = i * self.fmt_size * 2
+self.file.seek( offset )
+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:
+raise IndexError, e
+self._cached_ranges[i] = ( start, end )
+return start, end
+def __len__( self ):
+return self.length
+class RegionCoverage:
+def __init__( self, filename_base, profiler_info ):
+try:
+self._coverage = CachedRangesInFile( "%s.covered" % filename_base, profiler_info )
+except Exception, e:
+#print "Error loading coverage file %s: %s" % ( "%s.covered" % filename_base, e )
+self._coverage = []
+try:
+self._total_coverage = int( open( "%s.total_coverage" % filename_base ).read() )
+except Exception, e:
+#print "Error loading total coverage file %s: %s" % ( "%s.total_coverage" % filename_base, e )
+self._total_coverage = 0
+def get_start_index( self, start ):
+#binary search: returns index of range closest to start
+if start > self._coverage[-1][1]:
+return len( self._coverage ) - 1
+i = 0
+j = len( self._coverage) - 1
+while i < j:
+k = ( i + j ) / 2
+if start <= self._coverage[k][1]:
+j = k
+else:
+i = k + 1
+return i
+def get_coverage( self, start, end ):
+return self.get_coverage_regions_overlap( start, end )[0]
+def get_coverage_regions_overlap( self, start, end ):
+return self.get_coverage_regions_index_overlap( start, end )[0:2]
+def get_coverage_regions_index_overlap( self, start, end ):
+if len( self._coverage ) < 1 or start > self._coverage[-1][1] or end < self._coverage[0][0]:
+return 0, 0, 0
+if self._total_coverage and start <= self._coverage[0][0] and end >= self._coverage[-1][1]:
+return self._total_coverage, len( self._coverage ), 0
+coverage = 0
+region_count = 0
+start_index = self.get_start_index( start )
+for i in xrange( start_index, len( self._coverage ) ):
+c_start, c_end = self._coverage[i]
+if c_start > end:
+break
+if c_start <= end and c_end >= start:
+coverage += min( end, c_end ) - max( start, c_start )
+region_count += 1
+return coverage, region_count, start_index
+class CachedCoverageReader:
+def __init__( self, base_file_path, buffer = 10, table_names = None, profiler_info = None ):
+self._base_file_path = base_file_path
+self._buffer = buffer #number of chromosomes to keep in memory at a time
+self._coverage = {}
+if table_names is None: table_names = [ table_dir for table_dir in os.listdir( self._base_file_path ) if os.path.isdir( os.path.join( self._base_file_path, table_dir ) ) ]
+for tablename in table_names: self._coverage[tablename] = {}
+if profiler_info is None: profiler_info = {}
+self._profiler_info = profiler_info
+def iter_table_coverage_by_region( self, chrom, start, end ):
+for tablename, coverage, regions in self.iter_table_coverage_regions_by_region( chrom, start, end ):
+yield tablename, coverage
+def iter_table_coverage_regions_by_region( self, chrom, start, end ):
+for tablename, coverage, regions, index in self.iter_table_coverage_regions_index_by_region( chrom, start, end ):
+yield tablename, coverage, regions
+def iter_table_coverage_regions_index_by_region( self, chrom, start, end ):
+for tablename, chromosomes in self._coverage.iteritems():
+if chrom not in chromosomes:
+if len( chromosomes ) >= self._buffer:
+#randomly remove one chromosome from this table
+del chromosomes[ chromosomes.keys().pop( random.randint( 0, self._buffer - 1 ) ) ]
+chromosomes[chrom] = RegionCoverage( os.path.join ( self._base_file_path, tablename, chrom ), self._profiler_info )
+coverage, regions, index = chromosomes[chrom].get_coverage_regions_index_overlap( start, end )
+yield tablename, coverage, regions, index
+class TableCoverageSummary:
+def __init__( self, coverage_reader, chrom_lengths ):
+self.coverage_reader = coverage_reader
+self.chrom_lengths = chrom_lengths
+self.chromosome_coverage = {} #dict of bitset by chromosome holding user's collapsed input intervals
+self.total_interval_size = 0 #total size of user's input intervals
+self.total_interval_count = 0 #total number of user's input intervals
+self.table_coverage = {} #dict of total coverage by user's input intervals by table
+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.region_size_errors = {} #dictionary of lists of invalid ranges by chromosome
+def add_region( self, chrom, start, end ):
+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( 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] = {}
+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
+table_coverage = {} #dictionary of tables containing number of table bases overlaped by nr intervals
+interval_table_overlap_count = {} #dictionary of tables containing number of nr intervals overlaping table
+table_regions_overlap_count = {} #dictionary of tables containing number of regions overlaped (unique)
+interval_count = 0 #total number of nr intervals
+interval_size = 0 #holds total size of nr intervals
+region_start_end = {} #holds absolute start,end for each user input chromosome
+for chrom, chromosome_bitset in self.chromosome_coverage.iteritems():
+#loop through user's collapsed input intervals
+end = 0
+last_end_index = {}
+interval_size += chromosome_bitset.count_range()
+while True:
+if end >= chromosome_bitset.size: break
+start = chromosome_bitset.next_set( end )
+if start >= chromosome_bitset.size: break
+end = chromosome_bitset.next_clear( start )
+interval_count += 1
+if chrom not in region_start_end:
+region_start_end[chrom] = [start, end]
+else:
+region_start_end[chrom][1] = end
+for table_name, coverage, region_count, start_index in self.coverage_reader.iter_table_coverage_regions_index_by_region( chrom, start, end ):
+if table_name not in table_coverage:
+table_coverage[table_name] = 0
+interval_table_overlap_count[table_name] = 0
+table_regions_overlap_count[table_name] = 0
+table_coverage[table_name] += coverage
+if coverage:
+interval_table_overlap_count[table_name] += 1
+table_regions_overlap_count[table_name] += region_count
+if table_name in last_end_index and last_end_index[table_name] == start_index:
+table_regions_overlap_count[table_name] -= 1
+last_end_index[table_name] = start_index + region_count - 1
+table_region_coverage = {} #total coverage for tables by bounding nr interval region
+table_region_count = {} #total number for tables by bounding nr interval region
+for chrom, start_end in region_start_end.items():
+for table_name, coverage, region_count in self.coverage_reader.iter_table_coverage_regions_by_region( chrom, start_end[0], start_end[1] ):
+if table_name not in table_region_coverage:
+table_region_coverage[table_name] = 0
+table_region_count[table_name] = 0
+table_region_coverage[table_name] += coverage
+table_region_count[table_name] += region_count
+return table_region_coverage, table_region_count, interval_count, interval_size, table_coverage, table_regions_overlap_count, interval_table_overlap_count
+table_region_coverage, table_region_count, nr_interval_count, nr_interval_size, nr_table_coverage, nr_table_regions_overlap_count, nr_interval_table_overlap_count = get_nr_coverage()
+for table_name in self.table_coverage:
+#TODO: determine a type of statistic, then calculate and report here
+yield table_name, sum( self.table_chromosome_size.get( table_name, {} ).values() ), sum( self.table_chromosome_count.get( table_name, {} ).values() ), table_region_coverage.get( table_name, 0 ), table_region_count.get( table_name, 0 ), self.total_interval_count, self.total_interval_size,  self.table_coverage[table_name], self.table_regions_overlaped_count.get( table_name, 0), self.interval_table_overlap_count.get( table_name, 0 ), nr_interval_count, nr_interval_size, nr_table_coverage[table_name], nr_table_regions_overlap_count.get( table_name, 0 ), nr_interval_table_overlap_count.get( table_name, 0 )
+def profile_per_interval( interval_filename, chrom_col, start_col, end_col, out_filename, keep_empty, coverage_reader ):
+out = open( out_filename, 'wb' )
+for region in bx.intervals.io.NiceReaderWrapper( open( interval_filename, 'rb' ), chrom_col = chrom_col, start_col = start_col, end_col = end_col, fix_strand = True, return_header = False, return_comments = False ):
+for table_name, coverage, region_count in coverage_reader.iter_table_coverage_regions_by_region( region.chrom, region.start, region.end ):
+if keep_empty or coverage:
+#only output regions that have atleast 1 base covered unless empty are requested
+out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), table_name, coverage, region_count ) )
+out.close()
+def profile_summary( interval_filename, chrom_col, start_col, end_col, out_filename, keep_empty, coverage_reader, chrom_lengths ):
+out = open( out_filename, 'wb' )
+table_coverage_summary = TableCoverageSummary( coverage_reader, chrom_lengths )
+for region in bx.intervals.io.NiceReaderWrapper( open( interval_filename, 'rb' ), chrom_col = chrom_col, start_col = start_col, end_col = end_col, fix_strand = True, return_header = False, return_comments = False ):
+table_coverage_summary.add_region( region.chrom, region.start, region.end )
+out.write( "#tableName\ttableChromosomeCoverage\ttableChromosomeCount\ttableRegionCoverage\ttableRegionCount\tallIntervalCount\tallIntervalSize\tallCoverage\tallTableRegionsOverlaped\tallIntervalsOverlapingTable\tnrIntervalCount\tnrIntervalSize\tnrCoverage\tnrTableRegionsOverlaped\tnrIntervalsOverlapingTable\n" )
+for 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 in table_coverage_summary.iter_table_coverage():
+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()
+#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, profiler_info ):
+self.chroms = {}
+self.default_bitset_size = int( profiler_info.get( 'bitset_size', bx.bitset.MAX ) )
+chroms = profiler_info.get( 'chromosomes', None )
+if chroms:
+for chrom in chroms.split( ',' ):
+for fields in chrom.rsplit( '=', 1 ):
+if len( fields ) == 2:
+self.chroms[ fields[0] ] = int( fields[1] )
+else:
+self.chroms[ fields[0] ] = self.default_bitset_size
+def get( self, name ):
+return self.chroms.get( name, self.default_bitset_size )
+def parse_profiler_info( filename ):
+profiler_info = {}
+try:
+for line in open( filename ):
+fields = line.rstrip( '\n\r' ).split( '\t', 1 )
+if len( fields ) == 2:
+if fields[0] in profiler_info:
+if not isinstance( profiler_info[ fields[0] ], list ):
+profiler_info[ fields[0] ] = [ profiler_info[ fields[0] ] ]
+profiler_info[ fields[0] ].append( fields[1] )
+else:
+profiler_info[ fields[0] ] = fields[1]
+except:
+pass #likely missing file
+return profiler_info
+def __main__():
+parser = optparse.OptionParser()
+parser.add_option(
+'-k','--keep_empty',
+action="store_true",
+dest='keep_empty',
+default=False,
+help='Keep tables with 0 coverage'
+)
+parser.add_option(
+'-b','--buffer',
+dest='buffer',
+type='int',default=10,
+help='Number of Chromosomes to keep buffered'
+)
+parser.add_option(
+'-c','--chrom_col',
+dest='chrom_col',
+type='int',default=1,
+help='Chromosome column'
+)
+parser.add_option(
+'-s','--start_col',
+dest='start_col',
+type='int',default=2,
+help='Start Column'
+)
+parser.add_option(
+'-e','--end_col',
+dest='end_col',
+type='int',default=3,
+help='End Column'
+)
+parser.add_option(
+'-p','--path',
+dest='path',
+type='str',default='/galaxy/data/annotation_profiler/hg18',
+help='Path to profiled data for this organism'
+)
+parser.add_option(
+'-t','--table_names',
+dest='table_names',
+type='str',default='None',
+help='Table names requested'
+)
+parser.add_option(
+'-i','--input',
+dest='interval_filename',
+type='str',
+help='Input Interval File'
+)
+parser.add_option(
+'-o','--output',
+dest='out_filename',
+type='str',
+help='Input Interval File'
+)
+parser.add_option(
+'-S','--summary',
+action="store_true",
+dest='summary',
+default=False,
+help='Display Summary Results'
+)
+options, args = parser.parse_args()
+assert os.path.isdir( options.path ), IOError( "Configuration error: Table directory is missing (%s)" % options.path )
+#get profiler_info
+profiler_info = parse_profiler_info( os.path.join( options.path, 'profiler_info.txt' ) )
+table_names = options.table_names.split( "," )
+if table_names == ['None']: table_names = None
+coverage_reader = CachedCoverageReader( options.path, buffer = options.buffer, table_names = table_names, profiler_info = profiler_info )
+if options.summary:
+profile_summary( options.interval_filename, options.chrom_col - 1, options.start_col - 1, options.end_col -1, options.out_filename, options.keep_empty, coverage_reader, ChromosomeLengths( profiler_info ) )
+else:
+profile_per_interval( options.interval_filename, options.chrom_col - 1, options.start_col - 1, options.end_col -1, options.out_filename, options.keep_empty, coverage_reader )
+#print out data version info
+print 'Data version (%s:%s:%s)' % ( profiler_info.get( 'dbkey', 'unknown' ), profiler_info.get( 'profiler_hash', 'unknown' ), profiler_info.get( 'dump_time', 'unknown' ) )
+if __name__ == "__main__": __main__()

Mercurial > repos > devteam > annotation_profiler

comparison annotation_profiler_for_interval.py @ 0:3b33da018e74 draft default tip