def __main__():
maf_source_type = sys.argv.pop( 1 )
input_maf_filename = sys.argv[1].strip()
input_interval_filename = sys.argv[2].strip()
output_filename = sys.argv[3].strip()
dbkey = sys.argv[4].strip()
try:
chr_col = int( sys.argv[5].strip() ) - 1
start_col = int( sys.argv[6].strip() ) - 1
end_col = int( sys.argv[7].strip() ) - 1
except:
print >>sys.stderr, "You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file."
sys.exit()
summary = sys.argv[8].strip()
if summary.lower() == "true": summary = True
else: summary = False
mafIndexFile = "%s/maf_index.loc" % sys.argv[9]
try:
maf_index_filename = sys.argv[10].strip()
except:
maf_index_filename = None
index = index_filename = None
if maf_source_type == "user":
#index maf for use here
index, index_filename = maf_utilities.open_or_build_maf_index( input_maf_filename, maf_index_filename, species = [dbkey] )
if index is None:
print >>sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
elif maf_source_type == "cached":
#access existing indexes
index = maf_utilities.maf_index_by_uid( input_maf_filename, mafIndexFile )
if index is None:
print >> sys.stderr, "The MAF source specified (%s) appears to be invalid." % ( input_maf_filename )
sys.exit()
else:
print >>sys.stdout, 'Invalid source type specified: %s' % maf_source_type
sys.exit()
out = open(output_filename, 'w')
num_region = 0
species_summary = {}
total_length = 0
#loop through interval file
for num_region, region in enumerate( bx.intervals.io.NiceReaderWrapper( open( input_interval_filename, 'r' ), chrom_col = chr_col, start_col = start_col, end_col = end_col, fix_strand = True, return_header = False, return_comments = False ) ):
src = "%s.%s" % ( dbkey, region.chrom )
region_length = region.end - region.start
total_length += region_length
coverage = { dbkey: BitSet( region_length ) }
for block in maf_utilities.get_chopped_blocks_for_region( index, src, region, force_strand='+' ):
#make sure all species are known
for c in block.components:
spec = c.src.split( '.' )[0]
if spec not in coverage: coverage[spec] = BitSet( region_length )
start_offset, alignment = maf_utilities.reduce_block_by_primary_genome( block, dbkey, region.chrom, region.start )
for i in range( len( alignment[dbkey] ) ):
for spec, text in alignment.items():
if text[i] != '-':
coverage[spec].set( start_offset + i )
if summary:
#record summary
for key in coverage.keys():
if key not in species_summary: species_summary[key] = 0
species_summary[key] = species_summary[key] + coverage[key].count_range()
else:
#print coverage for interval
coverage_sum = coverage[dbkey].count_range()
out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), dbkey, coverage_sum, region_length - coverage_sum ) )
keys = coverage.keys()
keys.remove( dbkey )
keys.sort()
for key in keys:
coverage_sum = coverage[key].count_range()
out.write( "%s\t%s\t%s\t%s\n" % ( "\t".join( region.fields ), key, coverage_sum, region_length - coverage_sum ) )
if summary:
out.write( "#species\tnucleotides\tcoverage\n" )
for spec in species_summary:
out.write( "%s\t%s\t%.4f\n" % ( spec, species_summary[spec], float( species_summary[spec] ) / total_length ) )
out.close()
print "%i regions were processed with a total length of %i." % ( num_region, total_length )
maf_utilities.remove_temp_index_file( index_filename )
def __main__():
maf_source_type = sys.argv.pop(1)
input_maf_filename = sys.argv[1].strip()
input_interval_filename = sys.argv[2].strip()
output_filename = sys.argv[3].strip()
dbkey = sys.argv[4].strip()
try:
chr_col = int(sys.argv[5].strip()) - 1
start_col = int(sys.argv[6].strip()) - 1
end_col = int(sys.argv[7].strip()) - 1
except Exception:
print(
"You appear to be missing metadata. You can specify your metadata by clicking on the pencil icon associated with your interval file.",
file=sys.stderr)
sys.exit()
summary = sys.argv[8].strip()
if summary.lower() == "true":
summary = True
else:
summary = False
mafIndexFile = "%s/maf_index.loc" % sys.argv[9]
try:
maf_index_filename = sys.argv[10].strip()
except Exception:
maf_index_filename = None
index = index_filename = None
if maf_source_type == "user":
# index maf for use here
index, index_filename = maf_utilities.open_or_build_maf_index(
input_maf_filename, maf_index_filename, species=[dbkey])
if index is None:
print("Your MAF file appears to be malformed.", file=sys.stderr)
sys.exit()
elif maf_source_type == "cached":
# access existing indexes
index = maf_utilities.maf_index_by_uid(input_maf_filename,
mafIndexFile)
if index is None:
print("The MAF source specified (%s) appears to be invalid." %
(input_maf_filename),
file=sys.stderr)
sys.exit()
else:
print('Invalid source type specified: %s' % maf_source_type,
file=sys.stdout)
sys.exit()
out = open(output_filename, 'w')
num_region = None
num_bad_region = 0
species_summary = {}
total_length = 0
# loop through interval file
for num_region, region in enumerate(
bx.intervals.io.NiceReaderWrapper(
open(input_interval_filename, 'r'),
chrom_col=chr_col,
start_col=start_col,
end_col=end_col,
fix_strand=True,
return_header=False,
return_comments=False)): # noqa: B007
src = "%s.%s" % (dbkey, region.chrom)
region_length = region.end - region.start
if region_length < 1:
num_bad_region += 1
continue
total_length += region_length
coverage = {dbkey: BitSet(region_length)}
for block in index.get_as_iterator(src, region.start, region.end):
for spec in maf_utilities.get_species_in_block(block):
if spec not in coverage:
coverage[spec] = BitSet(region_length)
for block in maf_utilities.iter_blocks_split_by_species(block):
if maf_utilities.component_overlaps_region(
block.get_component_by_src(src), region):
# need to chop and orient the block
block = maf_utilities.orient_block_by_region(
maf_utilities.chop_block_by_region(block, src, region),
src,
region,
force_strand='+')
start_offset, alignment = maf_utilities.reduce_block_by_primary_genome(
block, dbkey, region.chrom, region.start)
for i in range(len(alignment[dbkey])):
for spec, text in alignment.items():
if text[i] != '-':
coverage[spec].set(start_offset + i)
if summary:
# record summary
for key in coverage.keys():
if key not in species_summary:
species_summary[key] = 0
species_summary[
key] = species_summary[key] + coverage[key].count_range()
else:
# print coverage for interval
coverage_sum = coverage[dbkey].count_range()
out.write("%s\t%s\t%s\t%s\n" %
("\t".join(region.fields), dbkey, coverage_sum,
region_length - coverage_sum))
keys = list(coverage.keys())
keys.remove(dbkey)
keys.sort()
for key in keys:
coverage_sum = coverage[key].count_range()
out.write("%s\t%s\t%s\t%s\n" %
("\t".join(region.fields), key, coverage_sum,
region_length - coverage_sum))
if summary:
out.write("#species\tnucleotides\tcoverage\n")
for spec in species_summary:
out.write("%s\t%s\t%.4f\n" %
(spec, species_summary[spec],
float(species_summary[spec]) / total_length))
out.close()
if num_region is not None:
print("%i regions were processed with a total length of %i." %
(num_region + 1, total_length))
if num_bad_region:
print("%i regions were invalid." % (num_bad_region))
maf_utilities.remove_temp_index_file(index_filename)