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