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) )
