def __main__():
print "Restricted to species:", sys.argv[1]
texts = {}
input_filename = sys.argv[2]
output_filename = sys.argv[3]
species = sys.argv[1].split(",")
if "None" in species:
species = maf_utilities.get_species_in_maf(input_filename)
file_out = open(output_filename, "w")
for spec in species:
file_out.write(">" + spec + "\n")
try:
for block in maf.Reader(open(input_filename, "r")):
component = block.get_component_by_src_start(spec)
if component:
file_out.write(component.text)
else:
file_out.write("-" * block.text_size)
except:
print >> sys.stderr, "Your MAF file appears to be malformed."
sys.exit()
file_out.write("\n")
file_out.close()
def __main__():
try:
species = maf_utilities.parse_species_option(sys.argv[1])
except Exception as e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
try:
input_filename = sys.argv[2]
except Exception as e:
maf_utilities.tool_fail("Error reading MAF filename: %s" % e)
try:
file_out = open(sys.argv[3], 'w')
except Exception as e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
if species:
print "Restricted to species: %s" % ', '.join(species)
else:
print "Not restricted to species."
if not species:
try:
species = maf_utilities.get_species_in_maf(input_filename)
except Exception as e:
maf_utilities.tool_fail(
"Error determining species in input MAF: %s" % e)
for spec in species:
file_out.write(">" + spec + "\n")
try:
for start_block in maf.Reader(open(input_filename, 'r')):
for block in maf_utilities.iter_blocks_split_by_species(
start_block):
block.remove_all_gap_columns() # remove extra gaps
component = block.get_component_by_src_start(
spec
) # blocks only have one occurrence of a particular species, so this is safe
if component:
file_out.write(component.text)
else:
file_out.write("-" * block.text_size)
except Exception as e:
maf_utilities.tool_fail(
"Your MAF file appears to be malformed: %s" % e)
file_out.write("\n")
file_out.close()
def __main__():
try:
species = maf_utilities.parse_species_option(sys.argv[1])
except Exception as e:
maf_utilities.tool_fail("Error determining species value: %s" % e)
try:
input_filename = sys.argv[2]
except Exception as e:
maf_utilities.tool_fail("Error reading MAF filename: %s" % e)
try:
file_out = open(sys.argv[3], 'w')
except Exception as e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
if species:
print("Restricted to species: %s" % ', '.join(species))
else:
print("Not restricted to species.")
if not species:
try:
species = maf_utilities.get_species_in_maf(input_filename)
except Exception as e:
maf_utilities.tool_fail("Error determining species in input MAF: %s" % e)
for spec in species:
file_out.write(">" + spec + "\n")
try:
for start_block in maf.Reader(open(input_filename, 'r')):
for block in maf_utilities.iter_blocks_split_by_species(start_block):
block.remove_all_gap_columns() # remove extra gaps
component = block.get_component_by_src_start(spec) # blocks only have one occurrence of a particular species, so this is safe
if component:
file_out.write(component.text)
else:
file_out.write("-" * block.text_size)
except Exception as e:
maf_utilities.tool_fail("Your MAF file appears to be malformed: %s" % e)
file_out.write("\n")
file_out.close()
input_filename = sys.argv[2]
except Exception, e:
maf_utilities.tool_fail("Error reading MAF filename: %s" % e)
try:
file_out = open(sys.argv[3], "w")
except Exception, e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
if species:
print "Restricted to species: %s" % ", ".join(species)
else:
print "Not restricted to species."
if not species:
try:
species = maf_utilities.get_species_in_maf(input_filename)
except Exception, e:
maf_utilities.tool_fail("Error determining species in input MAF: %s" % e)
for spec in species:
file_out.write(">" + spec + "\n")
try:
for start_block in maf.Reader(open(input_filename, "r")):
for block in maf_utilities.iter_blocks_split_by_species(start_block):
block.remove_all_gap_columns() # remove extra gaps
component = block.get_component_by_src_start(
spec
) # blocks only have one occurrence of a particular species, so this is safe
if component:
file_out.write(component.text)
else:
input_filename = sys.argv[2]
except Exception, e:
maf_utilities.tool_fail("Error reading MAF filename: %s" % e)
try:
file_out = open(sys.argv[3], 'w')
except Exception, e:
maf_utilities.tool_fail("Error opening file for output: %s" % e)
if species:
print "Restricted to species: %s" % ', '.join(species)
else:
print "Not restricted to species."
if not species:
try:
species = maf_utilities.get_species_in_maf(input_filename)
except Exception, e:
maf_utilities.tool_fail(
"Error determining species in input MAF: %s" % e)
for spec in species:
file_out.write(">" + spec + "\n")
try:
for start_block in maf.Reader(open(input_filename, 'r')):
for block in maf_utilities.iter_blocks_split_by_species(
start_block):
block.remove_all_gap_columns() #remove extra gaps
component = block.get_component_by_src_start(
spec
) #blocks only have one occurrence of a particular species, so this is safe
if component:
