print string.join(("# PREFIX", "npairs", "NPAIRS_MIN", "NPAIRS_MAX",
"NPAIRS_MEAN", "NPAIRS_MEDIAN", "NPAIRS_STDDEV"), "\t")
print string.join(("# PREFIX", "ppairs", "PPAIRS_MIN", "PPAIRS_MAX",
"PPAIRS_MEAN", "PPAIRS_MEDIAN", "PPAIRS_STDDEV"), "\t")
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)
"NFAILED_PAIRS", "NTOTAL_PAIRS", "PFAILED_PAIRS"), "\t")
print string.join(("# PREFIX", "npairs",
"NPAIRS_MIN", "NPAIRS_MAX", "NPAIRS_MEAN", "NPAIRS_MEDIAN", "NPAIRS_STDDEV"), "\t")
print string.join(("# PREFIX", "ppairs",
"PPAIRS_MIN", "PPAIRS_MAX", "PPAIRS_MEAN", "PPAIRS_MEDIAN", "PPAIRS_STDDEV"), "\t")
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)
"NEXONS_MEAN", "NEXONS_MEDIAN", "NEXONS_STDDEV")),
"\t".join(("species", "NSPECIES", "SPECIES_MAX", "MAX_PER_SPECIES",
"UNKNOWN")),
"\t".join(("failed", "NFAILED_SEQS", "NTOTAL_SEQS", "PFAILED_SEQS",
"NFAILED_PAIRS", "NTOTAL_PAIRS", "PFAILED_PAIRS")),
"\t".join(("npairs", "NPAIRS_MIN", "NPAIRS_MAX", "NPAIRS_MEAN",
"NPAIRS_MEDIAN", "NPAIRS_STDDEV")),
"\t".join(("ppairs", "PPAIRS_MIN", "PPAIRS_MAX", "PPAIRS_MEAN",
"PPAIRS_MEDIAN", "PPAIRS_STDDEV")),
"\t".join(("cov", "COV_MIN", "COV_MAX", "COV_MEAN", "COV_MEDIAN",
"COV_STDDEV")),
"\t".join(("pcov", "PCOV_MIN", "PCOV_MAX", "PCOV_MEAN", "PCOV_MEDIAN",
"PCOV_STDDEV")),
"\t".join(
("genepair", "STATUS", "COMPATIBILITY", "CMP_NEXONS", "REF_NEXONS",
Exons.ComparisonResult().GetHeader())),
"\t".join(("bootstrap", "NORGS", "NOTUS", "PTEST", "PTOTAL", "FTOTAL",
evaluate_bootstrap.Results().printHeader())),
]
if param_only_headers:
print "PREFIX\t" + "\nPREFIX\t".join(headers)
print E.GetFooter()
sys.exit(0)
else:
print "# PREFIX\t" + "\n# PREFIX\t".join(headers)
# 1. read multiple alignment in fasta format
all_mali, all_identifiers = MaliIO.readFasta(sys.stdin)
if len(all_identifiers) == 0: