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: