def __main__():
input_filename = sys.argv[1]
output_filename = sys.argv[2]
output_id = sys.argv[3]
# where to store files that become additional output
database_tmp_dir = sys.argv[4]
primary_spec = sys.argv[5]
species = sys.argv[6].split( ',' )
all_species = sys.argv[7].split( ',' )
partial = sys.argv[8]
keep_gaps = sys.argv[9]
out_files = {}
if "None" in species:
species = []
if primary_spec not in species:
species.append( primary_spec )
if primary_spec not in all_species:
all_species.append( primary_spec )
all_species.sort()
for spec in species:
if spec == primary_spec:
out_files[ spec ] = open( output_filename, 'wb+' )
else:
out_files[ spec ] = open( os.path.join( database_tmp_dir, 'primary_%s_%s_visible_interval_%s' % ( output_id, spec, spec ) ), 'wb+' )
out_files[ spec ].write( '#chrom\tstart\tend\tstrand\tscore\tname\t%s\n' % ( '\t'.join( all_species ) ) )
num_species = len( all_species )
file_in = open( input_filename, 'r' )
maf_reader = maf.Reader( file_in )
for i, m in enumerate( maf_reader ):
for j, block in enumerate( maf_utilities.iter_blocks_split_by_species( m ) ):
if len( block.components ) < num_species and partial == "partial_disallowed":
continue
sequences = {}
for c in block.components:
spec, chrom = maf_utilities.src_split( c.src )
if keep_gaps == 'remove_gaps':
sequences[ spec ] = c.text.replace( '-', '' )
else:
sequences[ spec ] = c.text
sequences = '\t'.join( [ sequences.get( _, '' ) for _ in all_species ] )
for spec in species:
c = block.get_component_by_src_start( spec )
if c is not None:
spec2, chrom = maf_utilities.src_split( c.src )
assert spec2 == spec, Exception( 'Species name inconsistancy found in component: %s != %s' % ( spec, spec2 ) )
out_files[ spec ].write( "%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % ( chrom, c.forward_strand_start, c.forward_strand_end, c.strand, m.score, "%s_%s_%s" % (spec, i, j), sequences ) )
file_in.close()
for file_out in out_files.values():
file_out.close()
def __main__():
index_location_file = sys.argv[1]
for i, line in enumerate(open(index_location_file)):
try:
if line.startswith('#'):
continue
display_name, uid, indexed_for_species, species_exist, maf_files = line.rstrip(
).split('\t')
indexed_for_species = indexed_for_species.split(',')
species_exist = species_exist.split(',')
maf_files = maf_files.split(',')
species_indexed_in_maf = []
species_found_in_maf = []
for maf_file in maf_files:
indexed_maf = bx.align.maf.MAFIndexedAccess(maf_file,
keep_open=True,
parse_e_rows=False)
for key in indexed_maf.indexes.indexes.keys():
spec = maf_utilities.src_split(key)[0]
if spec not in species_indexed_in_maf:
species_indexed_in_maf.append(spec)
while True: # reading entire maf set will take some time
block = indexed_maf.read_at_current_offset(indexed_maf.f)
if block is None:
break
for comp in block.components:
spec = maf_utilities.src_split(comp.src)[0]
if spec not in species_found_in_maf:
species_found_in_maf.append(spec)
# indexed species
for spec in indexed_for_species:
if spec not in species_indexed_in_maf:
print(
"Line %i, %s claims to be indexed for %s, but indexes do not exist."
% (i, uid, spec))
for spec in species_indexed_in_maf:
if spec not in indexed_for_species:
print(
"Line %i, %s is indexed for %s, but is not listed in loc file."
% (i, uid, spec))
# existing species
for spec in species_exist:
if spec not in species_found_in_maf:
print(
"Line %i, %s claims to have blocks for %s, but was not found in MAF files."
% (i, uid, spec))
for spec in species_found_in_maf:
if spec not in species_exist:
print(
"Line %i, %s contains %s, but is not listed in loc file."
% (i, uid, spec))
except Exception as e:
print("Line %i is invalid: %s" % (i, e))
def __main__():
index_location_file = sys.argv[ 1 ]
for i, line in enumerate( open( index_location_file ) ):
try:
if line.startswith( '#' ):
continue
display_name, uid, indexed_for_species, species_exist, maf_files = line.rstrip().split('\t')
indexed_for_species = indexed_for_species.split( ',' )
species_exist = species_exist.split( ',' )
maf_files = maf_files.split( ',' )
species_indexed_in_maf = []
species_found_in_maf = []
for maf_file in maf_files:
indexed_maf = bx.align.maf.MAFIndexedAccess( maf_file, keep_open=True, parse_e_rows=False )
for key in indexed_maf.indexes.indexes.keys():
spec = maf_utilities.src_split( key )[0]
if spec not in species_indexed_in_maf:
species_indexed_in_maf.append( spec )
while True: # reading entire maf set will take some time
block = indexed_maf.read_at_current_offset( indexed_maf.f )
if block is None:
break
for comp in block.components:
spec = maf_utilities.src_split( comp.src )[0]
if spec not in species_found_in_maf:
species_found_in_maf.append( spec )
# indexed species
for spec in indexed_for_species:
if spec not in species_indexed_in_maf:
print "Line %i, %s claims to be indexed for %s, but indexes do not exist." % ( i, uid, spec )
for spec in species_indexed_in_maf:
if spec not in indexed_for_species:
print "Line %i, %s is indexed for %s, but is not listed in loc file." % ( i, uid, spec )
# existing species
for spec in species_exist:
if spec not in species_found_in_maf:
print "Line %i, %s claims to have blocks for %s, but was not found in MAF files." % ( i, uid, spec )
for spec in species_found_in_maf:
if spec not in species_exist:
print "Line %i, %s contains %s, but is not listed in loc file." % ( i, uid, spec )
except Exception as e:
print "Line %i is invalid: %s" % ( i, e )
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__():
output_name = sys.argv.pop(1)
input_name = sys.argv.pop(1)
species = sys.argv.pop(1)
out = open(output_name,'w')
count = 0
#write interval header line
out.write( "#chrom\tstart\tend\tstrand\n" )
try:
for block in bx.align.maf.Reader( open( input_name, 'r' ) ):
for c in maf_utilities.iter_components_by_src_start( block, species ):
if c is not None:
out.write( "%s\t%i\t%i\t%s\n" % ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) )
count += 1
except Exception, e:
print >> sys.stderr, "There was a problem processing your input: %s" % e
def __main__():
output_name = sys.argv.pop(1)
input_name = sys.argv.pop(1)
count = 0
with open(output_name, 'w') as out:
for count, block in enumerate(bx.align.maf.Reader(open(input_name, 'r'))):
spec_counts = {}
for c in block.components:
spec, chrom = maf_utilities.src_split(c.src)
if spec not in spec_counts:
spec_counts[spec] = 0
else:
spec_counts[spec] += 1
out.write("%s\n" % maf_utilities.get_fasta_header(c, {'block_index' : count, 'species' : spec, 'sequence_index' : spec_counts[spec]}, suffix="%s_%i_%i" % (spec, count, spec_counts[spec])))
out.write("%s\n" % c.text)
out.write("\n")
print("%i MAF blocks converted to FASTA." % (count))
def __main__():
output_name = sys.argv.pop(1)
input_name = sys.argv.pop(1)
out = open( output_name, 'w' )
count = 0
for count, block in enumerate( bx.align.maf.Reader( open( input_name, 'r' ) ) ):
spec_counts = {}
for c in block.components:
spec, chrom = maf_utilities.src_split( c.src )
if spec not in spec_counts:
spec_counts[ spec ] = 0
else:
spec_counts[ spec ] += 1
out.write( "%s\n" % maf_utilities.get_fasta_header( c, { 'block_index' : count, 'species' : spec, 'sequence_index' : spec_counts[ spec ] }, suffix="%s_%i_%i" % ( spec, count, spec_counts[ spec ] ) ) )
out.write( "%s\n" % c.text )
out.write( "\n" )
out.close()
print "%i MAF blocks converted to FASTA." % ( count )
def __main__():
output_name = sys.argv.pop(1)
input_name = sys.argv.pop(1)
species = sys.argv.pop(1)
out = open(output_name, 'w')
count = 0
# write interval header line
out.write( "#chrom\tstart\tend\tstrand\n" )
try:
for block in bx.align.maf.Reader( open( input_name, 'r' ) ):
for c in maf_utilities.iter_components_by_src_start( block, species ):
if c is not None:
out.write( "%s\t%i\t%i\t%s\n" % ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) )
count += 1
except Exception as e:
print >> sys.stderr, "There was a problem processing your input: %s" % e
out.close()
print "%i MAF blocks converted to Genomic Intervals for species %s." % ( count, species )
def __main__():
output_name = sys.argv.pop(1)
input_name = sys.argv.pop(1)
species = sys.argv.pop(1)
count = 0
with open(output_name, 'w') as out:
# write interval header line
out.write("#chrom\tstart\tend\tstrand\n")
try:
with open(input_name, 'r') as fh:
for block in bx.align.maf.Reader(fh):
for c in maf_utilities.iter_components_by_src_start(block, species):
if c is not None:
out.write("%s\t%i\t%i\t%s\n" % (maf_utilities.src_split(c.src)[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand))
count += 1
except Exception as e:
print("There was a problem processing your input: %s" % e, file=sys.stderr)
print("%i MAF blocks converted to Genomic Intervals for species %s." % (count, species))
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()
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__()
