def __main__():
print "Restricted to species:", sys.argv[3]
input_filename = sys.argv[1]
output_filename = sys.argv[2]
species = sys.argv[3].split(",")
partial = sys.argv[4]
num_species = len(species)
file_in = open(input_filename, "r")
try:
maf_reader = maf.Reader(file_in)
file_out = open(output_filename, "w")
for block_num, block in enumerate(maf_reader):
if "None" not in species:
block = block.limit_to_species(species)
if len(block.components) < num_species and partial == "partial_disallowed":
continue
for component in block.components:
spec, chrom = maf.src_split(component.src)
if not spec or not chrom:
spec = chrom = component.src
file_out.write("%s\n" % maf_utilities.get_fasta_header(component, suffix="%s_%i" % (spec, block_num)))
file_out.write("%s\n" % component.text)
file_out.write("\n")
file_in.close()
except Exception, e:
print >> sys.stderr, "Your MAF file appears to be malformed:", e
sys.exit()
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)
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__():
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__()
