for line in infile: if line[0] == "#": continue if line[0] == ">": continue a, b = line[:-1].split("\t")[:2] if b not in components: components[b] = [] components[b].append(a) if param_loglevel >= 1: print "# read %i components." % len(components) if param_subset: components = {'all': string.split(param_subset, ",")} for key, identifiers in components.items(): # 1. remove gaps in multiple alignment mali = MaliIO.removeGappedColumns(MaliIO.getSubset(all_mali, identifiers), param_gap_char) for i in identifiers: print ">%s\n%s\n" % (i, mali[i]) if param_loglevel >= 1: print E.GetFooter() if __name__ == "__main__": sys.exit(main(sys.argv))
break infile.close() else: patterns = [] if param_loglevel > 1: print "# read %i bootstrap patterns" % len(patterns) for key, identifiers in components.items(): prefix = "%s%s_all" % (param_prefix, key) # 1. remove gaps in multiple alignment mali = MaliIO.removeGappedColumns( MaliIO.getSubset(all_mali, identifiers), param_gap_char) # 1. remove gaps in multiple alignment if param_do_cluster: matrix_overlap, matrix_total, coverages, matrix_identity = GetOverlapMatrix( mali, identifiers) matrix_coverage = ((100.0 * matrix_overlap) / matrix_total) if param_loglevel >= 3: print "# overlap\n", matrix_overlap print "# total\n", matrix_total print "# coverage\n", matrix_coverage print "# coverages\n", coverages print "# identity\n", matrix_identity
print string.join(("# PREFIX", "cov", "COV_MIN", "COV_MAX", "COV_MEAN", "COV_MEDIAN", "COV_STDDEV"), "\t") print string.join(("# PREFIX", "pcov", "PCOV_MIN", "PCOV_MAX", "PCOV_MEAN", "PCOV_MEDIAN", "PCOV_STDDEV"), "\t") print string.join(("# PREFIX", "genepair", "STATUS", "COMPATIBILITY", "CMP_NEXONS", "REF_NEXONS", Exons.ComparisonResult().GetHeader()), "\t") for key, identifiers in components.items(): prefix = "%s%s_all" % (param_prefix, key) # 1. remove gaps in multiple alignment mali = MaliIO.removeGappedColumns( MaliIO.getSubset(all_mali, identifiers), param_gap_char) # 1. remove gaps in multiple alignment if param_do_cluster: matrix_overlap, matrix_total, coverages = GetOverlapMatrix( mali, identifiers) matrix_coverage = 100 - ((100 * matrix_overlap) / matrix_total) if param_loglevel >= 3: print "# overlap\n", matrix_overlap print "# total\n", matrix_total print "# coverage\n", matrix_coverage print "# coverages\n", coverages matrix_compatibility = WriteGeneStructureCorrespondence(
for line in infile: if line[0] == "#": continue if line[0] == ">": continue a, b = line[:-1].split("\t")[:2] if b not in components: components[b] = [] components[b].append(a) if param_loglevel >= 1: print "# read %i components." % len(components) if param_subset: components = {'all': string.split(param_subset, ",")} for key, identifiers in components.items(): # 1. remove gaps in multiple alignment mali = MaliIO.removeGappedColumns( MaliIO.getSubset(all_mali, identifiers), param_gap_char) for i in identifiers: print ">%s\n%s\n" % (i, mali[i]) if param_loglevel >= 1: print E.GetFooter() if __name__ == "__main__": sys.exit(main(sys.argv))
print string.join( ("# PREFIX", "cov", "COV_MIN","COV_MAX","COV_MEAN","COV_MEDIAN","COV_STDDEV"), "\t") print string.join( ("# PREFIX", "pcov", "PCOV_MIN","PCOV_MAX","PCOV_MEAN","PCOV_MEDIAN","PCOV_STDDEV"), "\t") print string.join( ("# PREFIX", "genepair", "STATUS", "COMPATIBILITY", "CMP_NEXONS", "REF_NEXONS", Exons.ComparisonResult().GetHeader()), "\t") for key, identifiers in components.items(): prefix = "%s%s_all" % (param_prefix, key) ## 1. remove gaps in multiple alignment mali = MaliIO.removeGappedColumns( MaliIO.getSubset( all_mali, identifiers), param_gap_char ) ## 1. remove gaps in multiple alignment if param_do_cluster: matrix_overlap, matrix_total, coverages = GetOverlapMatrix( mali, identifiers) matrix_coverage = 100 - ((100 * matrix_overlap) / matrix_total) if param_loglevel >= 3: print "# overlap\n", matrix_overlap print "# total\n", matrix_total print "# coverage\n", matrix_coverage print "# coverages\n", coverages matrix_compatibility = WriteGeneStructureCorrespondence( mali, identifiers, exons, param_master_pattern, prefix = prefix )
patterns, num_samples=evaluate_bootstrap.ReadPatterns( infile ) break infile.close() else: patterns = [] if param_loglevel >1: print "# read %i bootstrap patterns" % len(patterns) for key, identifiers in components.items(): prefix = "%s%s_all" % (param_prefix, key) ## 1. remove gaps in multiple alignment mali = MaliIO.removeGappedColumns( MaliIO.getSubset( all_mali, identifiers), param_gap_char ) ## 1. remove gaps in multiple alignment if param_do_cluster: matrix_overlap, matrix_total, coverages, matrix_identity = GetOverlapMatrix( mali, identifiers) matrix_coverage = ((100.0 * matrix_overlap) / matrix_total) if param_loglevel >= 3: print "# overlap\n", matrix_overlap print "# total\n", matrix_total print "# coverage\n", matrix_coverage print "# coverages\n", coverages print "# identity\n", matrix_identity if param_loglevel >= 5:
for line in infile: if line[0] == "#": continue if line[0] == ">": continue a, b = line[:-1].split("\t")[:2] if b not in components: components[b] = [] components[b].append(a) if param_loglevel >= 1: print "# read %i components." % len(components) if param_subset: components = { 'all' : string.split( param_subset, "," ) } for key, identifiers in components.items(): # 1. remove gaps in multiple alignment mali = MaliIO.removeGappedColumns( MaliIO.getSubset( all_mali, identifiers), param_gap_char ) for i in identifiers: print ">%s\n%s\n" % (i, mali[i] ) if param_loglevel >= 1: print E.GetFooter() if __name__ == "__main__": sys.exit( main( sys.argv) )