def main():
species = maf_utilities.parse_species_option( sys.argv[1] )
if species:
spec_len = len( species )
else:
spec_len = 0
try:
maf_reader = bx.align.maf.Reader( open( sys.argv[2], 'r' ) )
maf_writer = bx.align.maf.Writer( open( sys.argv[3], 'w' ) )
except:
print("Your MAF file appears to be malformed.", file=sys.stderr)
sys.exit()
allow_partial = False
if int( sys.argv[4] ):
allow_partial = True
min_species_per_block = int( sys.argv[5] )
maf_blocks_kept = 0
for m in maf_reader:
if species:
m = m.limit_to_species( species )
m.remove_all_gap_columns()
spec_in_block_len = len( maf_utilities.get_species_in_block( m ) )
if ( not species or allow_partial or spec_in_block_len == spec_len ) and spec_in_block_len > min_species_per_block:
maf_writer.write( m )
maf_blocks_kept += 1
maf_reader.close()
maf_writer.close()
print("Restricted to species: %s." % ", ".join( species ))
print("%i MAF blocks have been kept." % maf_blocks_kept)
def main():
species = maf_utilities.parse_species_option(sys.argv[1])
if species:
spec_len = len(species)
else:
spec_len = 0
try:
maf_reader = bx.align.maf.Reader(open(sys.argv[2], 'r'))
maf_writer = bx.align.maf.Writer(open(sys.argv[3], 'w'))
except Exception:
print("Your MAF file appears to be malformed.", file=sys.stderr)
sys.exit()
allow_partial = False
if int(sys.argv[4]):
allow_partial = True
min_species_per_block = int(sys.argv[5])
maf_blocks_kept = 0
for m in maf_reader:
if species:
m = m.limit_to_species(species)
m.remove_all_gap_columns()
spec_in_block_len = len(maf_utilities.get_species_in_block(m))
if (not species or allow_partial or spec_in_block_len == spec_len) and spec_in_block_len > min_species_per_block:
maf_writer.write(m)
maf_blocks_kept += 1
maf_reader.close()
maf_writer.close()
print("Restricted to species: %s." % ", ".join(species))
print("%i MAF blocks have been kept." % maf_blocks_kept)
def __main__():
try:
maf_reader = maf.Reader(open(sys.argv[1]))
except Exception as e:
maf_utilities.tool_fail("Error opening input MAF: %s" % e)
try:
file_out = open(sys.argv[2], 'w')
except Exception as e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
try:
species = maf_utilities.parse_species_option(sys.argv[3])
if species:
num_species = len(species)
else:
num_species = 0
except Exception as e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
try:
partial = sys.argv[4]
except Exception as e:
maf_utilities.tool_fail("Error determining keep partial value: %s" % e)
if species:
print("Restricted to species: %s" % ', '.join(species))
else:
print("Not restricted to species.")
for block_num, block in enumerate(maf_reader):
if species:
block = block.limit_to_species(species)
if len(maf_utilities.get_species_in_block(
block)) < num_species and partial == "partial_disallowed":
continue
spec_counts = {}
for component in block.components:
spec, chrom = maf_utilities.src_split(component.src)
if spec not in spec_counts:
spec_counts[spec] = 0
else:
spec_counts[spec] += 1
file_out.write("%s\n" % maf_utilities.get_fasta_header(
component, {
'block_index': block_num,
'species': spec,
'sequence_index': spec_counts[spec]
},
suffix="%s_%i_%i" % (spec, block_num, spec_counts[spec])))
file_out.write("%s\n" % component.text)
file_out.write("\n")
file_out.close()
def __main__():
try:
maf_reader = maf.Reader(open(sys.argv[1]))
except Exception as e:
maf_utilities.tool_fail("Error opening input MAF: %s" % e)
try:
file_out = open(sys.argv[2], 'w')
except Exception as e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
try:
species = maf_utilities.parse_species_option(sys.argv[3])
if species:
num_species = len(species)
else:
num_species = 0
except Exception as e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
try:
partial = sys.argv[4]
except Exception as e:
maf_utilities.tool_fail("Error determining keep partial value: %s" % e)
if species:
print("Restricted to species: %s" % ', '.join(species))
else:
print("Not restricted to species.")
for block_num, block in enumerate(maf_reader):
if species:
block = block.limit_to_species(species)
if len(maf_utilities.get_species_in_block(block)) < num_species and partial == "partial_disallowed":
continue
spec_counts = {}
for component in block.components:
spec, chrom = maf_utilities.src_split(component.src)
if spec not in spec_counts:
spec_counts[spec] = 0
else:
spec_counts[spec] += 1
d = OrderedDict([('block_index', block_num), ('species', spec), ('sequence_index', spec_counts[spec])])
file_out.write("%s\n" % maf_utilities.get_fasta_header(component, d, suffix="%s_%i_%i" % (spec, block_num, spec_counts[spec])))
file_out.write("%s\n" % component.text)
file_out.write("\n")
file_out.close()
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)
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("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:
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 ) ):
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 )
num_species = 0
except Exception, e:
maf_utilities.tool_fail( "Error determining species value: %s" % e )
try:
partial = sys.argv[4]
except Exception, e:
maf_utilities.tool_fail( "Error determining keep partial value: %s" % e )
if species:
print "Restricted to species: %s" % ', '.join( species )
else:
print "Not restricted to species."
for block_num, block in enumerate( maf_reader ):
if species:
block = block.limit_to_species( species )
if len( maf_utilities.get_species_in_block( block ) ) < num_species and partial == "partial_disallowed": continue
spec_counts = {}
for component in block.components:
spec, chrom = maf_utilities.src_split( component.src )
if spec not in spec_counts:
spec_counts[ spec ] = 0
else:
spec_counts[ spec ] += 1
file_out.write( "%s\n" % maf_utilities.get_fasta_header( component, { 'block_index' : block_num, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix = "%s_%i_%i" % ( spec, block_num, spec_counts[ spec ] ) ) )
file_out.write( "%s\n" % component.text )
file_out.write( "\n" )
file_out.close()
if __name__ == "__main__": __main__()
