def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: codemls2tsv.py 2781 2009-09-10 11:33:14Z andreas $"
)
parser.add_option("--methods",
dest="methods",
type="choice",
action="append",
choices=("summary-numbers", "jalview",
"positive-site-table", "positive-site-list",
"count-positive-sites"),
help="methods for analysis.")
parser.add_option("--selection-mode",
dest="selection_mode",
type="choice",
choices=("all", "consistent", "emes"),
help="how to select positive sites.")
parser.add_option("--prefix",
dest="prefix",
type="string",
help="prefix for rows.")
parser.add_option("--pattern-input-filenames",
dest="pattern_input_filenames",
type="string",
help="input pattern.")
parser.add_option(
"--filter-probability",
dest="filter_probability",
type="float",
help=
"threshold for probability above which to include positive sites [default=%default]."
)
parser.add_option(
"--filter-omega",
dest="filter_omega",
type="float",
help=
"threshold for omega above which to include positive sites [default=%default]."
)
parser.add_option("--models",
dest="models",
type="string",
help="restrict output to set of site specific models.")
parser.add_option("--analysis",
dest="analysis",
type="string",
help="restrict output to set of analysis [beb|neb].")
parser.add_option("--significance-threshold",
dest="significance_threshold",
type="float",
help="significance threshold for log-likelihood test.")
parser.add_option("--filter-mali",
dest="filter_mali",
type="choice",
choices=("none", "gaps"),
help="filter by mali to remove gapped positions.")
parser.add_option(
"--filename-mali",
dest="filename_mali",
type="string",
help=
"filename with multiple alignment used for calculating sites - used for filtering"
)
parser.add_option(
"--filename-map-mali",
dest="filename_map_mali",
type="string",
help="filename with multiple alignment to map sites onto.")
parser.add_option(
"--jalview-titles",
dest="jalview_titles",
type="string",
help="comma separated list of jalview annotation titles.")
parser.add_option("--jalview-symbol",
dest="jalview_symbol",
type="string",
help="symbol to use in jalview.")
parser.set_defaults(
methods=[],
prefix=None,
filter_probability=0,
filter_omega=0,
models="",
analysis="",
significance_threshold=0.05,
selection_mode="consistent",
filename_mali=None,
filename_map_mali=None,
jalview_symbol="*",
jalview_titles="",
filter_mali=None,
)
(options, args) = E.Start(parser)
if options.jalview_titles:
options.jalview_titles = options.jalview_titles.split(",")
else:
options.jalview_titles = args
options.models = options.models.split(",")
options.analysis = options.analysis.split(",")
for a in options.analysis:
if a not in ("beb", "neb"):
raise "unknown analysis section: '%s', possible values are 'beb' and/or 'neb'" % a
for a in options.models:
if a not in ("8", "2", "3"):
raise "unknown model: '%s', possible values are 2, 3, 8" % a
codeml = WrapperCodeML.CodeMLSites()
## filter and extract functions
filter_f = lambda x: x.mProbability >= options.filter_probability and x.mOmega >= options.filter_omega
extract_f = lambda x: x.mResidue
## read multiple results
results = []
ninput, noutput, nskipped = 0, 0, 0
headers = []
for f in args:
ninput += 1
try:
results.append(codeml.parseOutput(open(f, "r").readlines()))
except WrapperCodeML.UsageError:
if options.loglevel >= 1:
options.stdlog.write("# no input from %s\n" % f)
nskipped += 1
continue
noutput += 1
headers.append(f)
## map of nested model (key) to more general model
map_nested_models = {'8': '7', '2': '1', '3': '0'}
if options.filename_mali:
mali = Mali.Mali()
mali.readFromFile(open(options.filename_mali, "r"))
else:
mali = None
###############################################################
###############################################################
###############################################################
## use multiple alignment to map residues to a reference mali
## or a sequence.
###############################################################
if options.filename_map_mali:
if not mali:
raise "please supply the input multiple alignment, if residues are to be mapped."
## translate the alignments
def translate(s):
sequence = s.mString
seq = []
for codon in [
sequence[x:x + 3] for x in range(0, len(sequence), 3)
]:
aa = Genomics.MapCodon2AA(codon)
seq.append(aa)
s.mString = "".join(seq)
tmali = Mali.Mali()
tmali.readFromFile(open(options.filename_mali, "r"))
tmali.apply(translate)
tmap_mali = Mali.Mali()
tmap_mali.readFromFile(open(options.filename_map_mali, "r"))
if tmap_mali.getAlphabet() == "na":
tmap_mali.apply(translate)
map_old2new = alignlib_lite.py_makeAlignmentVector()
mali1 = alignlib_lite.py_makeProfileFromMali(convertMali2Mali(tmali))
if tmap_mali.getLength() == 1:
s = tmap_mali.values()[0].mString
mali2 = alignlib_lite.py_makeSequence(s)
## see if you can find an identical subsequence and then align to thisD
for x in tmali.values():
if s in re.sub("[- .]+", "", x.mString):
mali1 = alignlib_lite.py_makeSequence(x.mString)
break
else:
mali2 = alignlib_lite.py_makeProfileFromMali(
convertMali2Mali(tmap_mali))
alignator = alignlib_lite.py_makeAlignatorDPFull(
alignlib_lite.py_ALIGNMENT_LOCAL, -10.0, -2.0)
alignator.align(map_old2new, mali1, mali2)
consensus = tmap_mali.getConsensus()
if options.loglevel >= 4:
options.stdlog.write("# alphabet: %s\n" % tmap_mali.getAlphabet())
options.stdlog.write("# orig : %s\n" % tmali.getConsensus())
options.stdlog.write("# mapped: %s\n" % consensus)
options.stdlog.write("# alignment: %s\n" % map_old2new.Write())
else:
map_old2new = None
for method in options.methods:
if method == "summary-numbers":
options.stdlog.write( \
"""# Numbers of positive sites.
#
# The consistent row/column contains positive sites that are significant
# (above thresholds for probability and omega) for all models/analysis
# that have been selected (label: cons).
#
# The log-likelihood ratio test is performed for model pairs, depending
# on the output chosen.
# Significance threshold: %6.4f
# The pairs are 8 versus 7 and 2 versus 1 and 3 versus 0.
#
""" % options.significance_threshold )
## write header
if options.prefix: options.stdout.write("prefix\t")
options.stdout.write("method\tnseq\t")
h = []
for model in options.models:
for analysis in options.analysis:
h.append("%s%s" % (analysis, model))
h.append("p%s" % (model))
h.append("df%s" % (model))
h.append("chi%s" % (model))
h.append("lrt%s" % (model))
options.stdout.write("\t".join(h))
options.stdout.write("\tcons\tpassed\tfilename\n")
nmethod = 0
consistent_cols = [None for x in range(len(options.analysis))]
passed_tests = {}
for m in options.models:
passed_tests[m] = 0
for result in results:
row_consistent = None
if options.prefix:
options.stdout.write("%s" % (options.prefix))
options.stdout.write("%i" % nmethod)
options.stdout.write("\t%i" % (result.mNumSequences))
npassed = 0
for model in options.models:
sites = result.mSites[model]
## do significance test
full_model, null_model = model, map_nested_models[model]
lrt = Stats.doLogLikelihoodTest(
result.mSites[full_model].mLogLikelihood,
result.mSites[full_model].mNumParameters,
result.mSites[null_model].mLogLikelihood,
result.mSites[null_model].mNumParameters,
options.significance_threshold)
x = 0
for analysis in options.analysis:
if analysis == "neb":
s = set(
map(
extract_f,
filter(filter_f,
sites.mNEB.mPositiveSites)))
elif analysis == "beb":
s = set(
map(
extract_f,
filter(filter_f,
sites.mBEB.mPositiveSites)))
options.stdout.write("\t%i" % (len(s)))
if not lrt.mPassed:
s = set()
if row_consistent == None:
row_consistent = s
else:
row_consistent = row_consistent.intersection(s)
if consistent_cols[x] == None:
consistent_cols[x] = s
else:
consistent_cols[x] = consistent_cols[
x].intersection(s)
x += 1
if lrt.mPassed:
c = "passed"
passed_tests[model] += 1
npassed += 1
else:
c = "failed"
options.stdout.write("\t%5.2e\t%i\t%5.2f\t%s" %\
(lrt.mProbability,
lrt.mDegreesFreedom,
lrt.mChiSquaredValue,
c))
options.stdout.write(
"\t%i\t%i\t%s\n" %
(len(row_consistent), npassed, headers[nmethod]))
nmethod += 1
if options.prefix:
options.stdout.write("%s\t" % options.prefix)
options.stdout.write("cons")
row_consistent = None
total_passed = 0
for model in options.models:
x = 0
for analysis in options.analysis:
s = consistent_cols[x]
if s == None:
s = set()
options.stdout.write("\t%i" % (len(s)))
if row_consistent == None:
row_consistent = s
else:
row_consistent = row_consistent.intersection(s)
x += 1
options.stdout.write("\tna\t%i" % passed_tests[model])
total_passed += passed_tests[model]
options.stdout.write("\t%i\t%i\n" %
(len(row_consistent), total_passed))
elif method == "jalview":
options.stdout.write("JALVIEW_ANNOTATION\n")
options.stdout.write("# Created: %s\n\n" %
(time.asctime(time.localtime(time.time()))))
l = 1
x = 0
for result in results:
sites, significance = selectPositiveSites(
[result], options.selection_mode, options, mali)
codes = [""] * result.mLength
if len(sites) == 0: continue
for site in sites:
codes[site - 1] = options.jalview_symbol
options.stdout.write(
"NO_GRAPH\t%s\t%s\n" %
(options.jalview_titles[x], "|".join(codes)))
x += 1
elif method == "count-positive-sites":
sites, significance = selectPositiveSites(results,
options.selection_mode,
options, mali)
options.stdout.write("%i\n" % (len(sites)))
elif method in ("positive-site-table", ):
sites, significance = selectPositiveSites(results,
options.selection_mode,
options, mali)
headers = ["site", "P"]
if map_old2new:
headers.append("mapped")
headers.append("Pm")
options.stdout.write("\t".join(headers) + "\n")
sites = list(sites)
sites.sort()
nmapped, nunmapped = 0, 0
for site in sites:
values = [site, "%6.4f" % significance[site]]
if map_old2new:
r = map_old2new.mapRowToCol(site)
if r == 0:
values.append("na")
values.append("")
nunmapped += 1
if options.loglevel >= 2:
options.stdlog.write("# unmapped residue: %i\n" %
site)
else:
values.append(r)
values.append(consensus[r - 1])
nmapped += 1
options.stdout.write("\t".join(map(str, (values))) + "\n")
if options.loglevel >= 1:
options.stdlog.write(
"# sites: ninput=%i, noutput=%i, nskipped=%i\n" %
(len(sites), nmapped, nunmapped))
E.info("ninput=%i, noutput=%i, nskipped=%i" % (ninput, noutput, nskipped))
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id: sequences2mali.py 2782 2009-09-10 11:40:29Z andreas $", usage=globals()["__doc__"])
parser.add_option("-i", "--input-format", dest="input_format", type="choice",
choices=(
"plain", "fasta", "clustal", "stockholm", "phylip"),
help="input format of multiple alignment")
parser.add_option("-o", "--output-format", dest="output_format", type="choice",
choices=("plain", "fasta", "stockholm", "phylip"),
help="output format of multiple alignment")
parser.add_option("-m", "--method", dest="method", type="choice",
choices=("add",),
help="""method to use to build multiple alignment.""")
parser.add_option("-p", "--parameters", dest="parameters", type="string",
help="parameter stack for methods that require one.")
parser.add_option("-a", "--alignment-method", dest="alignment_method", type="choice",
choices=("sw", "nw"),
help="alignment_method [%default].")
parser.set_defaults(
input_format="fasta",
output_format="fasta",
method=None,
parameters="",
gop=-10.0,
gep=-1.0,
alignment_method="sw",
)
(options, args) = E.Start(parser)
options.parameters = options.parameters.split(",")
iterator = FastaIterator.iterate(sys.stdin)
if options.method == "add":
mali = Mali.Mali()
mali.readFromFile(
open(options.parameters[0], "r"), format=options.input_format)
del options.parameters[0]
old_length = mali.getLength()
new_mali = convertMali2Mali(mali)
if options.alignment_method == "sw":
alignator = alignlib_lite.py_makeAlignatorFullDP(
options.gop, options.gep)
else:
alignator = alignlib_lite.py_makeAlignatorFullDPGlobal(
options.gop, options.gep)
while 1:
cur_record = iterator.next()
if cur_record is None:
break
map_mali2seq = alignlib_lite.py_makeAlignataVector()
sequence = alignlib_lite.py_makeSequence(cur_record.sequence)
profile = alignlib_lite.py_makeProfileFromMali(new_mali)
if options.loglevel >= 4:
options.stdlog.write(profile.Write())
alignator.Align(profile, sequence, map_mali2seq)
if options.loglevel >= 3:
options.stdlog.write(map_mali2seq.Write())
# add sequence to mali
a = alignlib_lite.py_makeAlignatumFromString(cur_record.sequence)
a.thisown = 0
new_mali.addAlignatum(a, map_mali2seq, 1, 1, 1, 1, 1)
id = cur_record.title
mali.mIdentifiers.append(id)
mali.mMali[id] = Mali.AlignedString(id, 0, len(
cur_record.sequence), new_mali.getRow(new_mali.getWidth() - 1).getString())
# substitute
for x in range(old_length):
mali.mMali[mali.mIdentifiers[x]].mString = new_mali.getRow(
x).getString()
mali.writeToFile(sys.stdout, format=options.output_format)
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version="%prog version: $Id: codemls2tsv.py 2781 2009-09-10 11:33:14Z andreas $")
parser.add_option("--methods", dest="methods", type="choice", action="append",
choices=("summary-numbers", "jalview",
"positive-site-table", "positive-site-list",
"count-positive-sites"),
help="methods for analysis.")
parser.add_option("--selection-mode", dest="selection_mode", type="choice",
choices=("all", "consistent", "emes"),
help="how to select positive sites.")
parser.add_option("--prefix", dest="prefix", type="string",
help="prefix for rows.")
parser.add_option("--pattern-input-filenames", dest="pattern_input_filenames", type="string",
help="input pattern.")
parser.add_option("--filter-probability", dest="filter_probability", type="float",
help="threshold for probability above which to include positive sites [default=%default].")
parser.add_option("--filter-omega", dest="filter_omega", type="float",
help="threshold for omega above which to include positive sites [default=%default].")
parser.add_option("--models", dest="models", type="string",
help="restrict output to set of site specific models.")
parser.add_option("--analysis", dest="analysis", type="string",
help="restrict output to set of analysis [beb|neb].")
parser.add_option("--significance-threshold", dest="significance_threshold", type="float",
help="significance threshold for log-likelihood test.")
parser.add_option("--filter-mali", dest="filter_mali", type="choice",
choices=("none", "gaps"),
help="filter by mali to remove gapped positions.")
parser.add_option("--filename-mali", dest="filename_mali", type="string",
help="filename with multiple alignment used for calculating sites - used for filtering")
parser.add_option("--filename-map-mali", dest="filename_map_mali", type="string",
help="filename with multiple alignment to map sites onto.")
parser.add_option("--jalview-titles", dest="jalview_titles", type="string",
help="comma separated list of jalview annotation titles.")
parser.add_option("--jalview-symbol", dest="jalview_symbol", type="string",
help="symbol to use in jalview.")
parser.set_defaults(
methods=[],
prefix=None,
filter_probability=0,
filter_omega=0,
models="",
analysis="",
significance_threshold=0.05,
selection_mode="consistent",
filename_mali=None,
filename_map_mali=None,
jalview_symbol="*",
jalview_titles="",
filter_mali=None,
)
(options, args) = E.Start(parser)
if options.jalview_titles:
options.jalview_titles = options.jalview_titles.split(",")
else:
options.jalview_titles = args
options.models = options.models.split(",")
options.analysis = options.analysis.split(",")
for a in options.analysis:
if a not in ("beb", "neb"):
raise "unknown analysis section: '%s', possible values are 'beb' and/or 'neb'" % a
for a in options.models:
if a not in ("8", "2", "3"):
raise "unknown model: '%s', possible values are 2, 3, 8" % a
codeml = WrapperCodeML.CodeMLSites()
# filter and extract functions
filter_f = lambda x: x.mProbability >= options.filter_probability and x.mOmega >= options.filter_omega
extract_f = lambda x: x.mResidue
# read multiple results
results = []
ninput, noutput, nskipped = 0, 0, 0
headers = []
for f in args:
ninput += 1
try:
results.append(codeml.parseOutput(open(f, "r").readlines()))
except WrapperCodeML.UsageError:
if options.loglevel >= 1:
options.stdlog.write("# no input from %s\n" % f)
nskipped += 1
continue
noutput += 1
headers.append(f)
# map of nested model (key) to more general model
map_nested_models = {'8': '7',
'2': '1',
'3': '0'}
if options.filename_mali:
mali = Mali.Mali()
mali.readFromFile(open(options.filename_mali, "r"))
else:
mali = None
###############################################################
###############################################################
###############################################################
# use multiple alignment to map residues to a reference mali
# or a sequence.
###############################################################
if options.filename_map_mali:
if not mali:
raise "please supply the input multiple alignment, if residues are to be mapped."
# translate the alignments
def translate(s):
sequence = s.mString
seq = []
for codon in [sequence[x:x + 3] for x in range(0, len(sequence), 3)]:
aa = Genomics.MapCodon2AA(codon)
seq.append(aa)
s.mString = "".join(seq)
tmali = Mali.Mali()
tmali.readFromFile(open(options.filename_mali, "r"))
tmali.apply(translate)
tmap_mali = Mali.Mali()
tmap_mali.readFromFile(open(options.filename_map_mali, "r"))
if tmap_mali.getAlphabet() == "na":
tmap_mali.apply(translate)
map_old2new = alignlib_lite.py_makeAlignmentVector()
mali1 = alignlib_lite.py_makeProfileFromMali(convertMali2Mali(tmali))
if tmap_mali.getLength() == 1:
s = tmap_mali.values()[0].mString
mali2 = alignlib_lite.py_makeSequence(s)
# see if you can find an identical subsequence and then align to
# thisD
for x in tmali.values():
if s in re.sub("[- .]+", "", x.mString):
mali1 = alignlib_lite.py_makeSequence(x.mString)
break
else:
mali2 = alignlib_lite.py_makeProfileFromMali(
convertMali2Mali(tmap_mali))
alignator = alignlib_lite.py_makeAlignatorDPFull(
alignlib_lite.py_ALIGNMENT_LOCAL, -10.0, -2.0)
alignator.align(map_old2new, mali1, mali2)
consensus = tmap_mali.getConsensus()
if options.loglevel >= 4:
options.stdlog.write("# alphabet: %s\n" % tmap_mali.getAlphabet())
options.stdlog.write("# orig : %s\n" % tmali.getConsensus())
options.stdlog.write("# mapped: %s\n" % consensus)
options.stdlog.write("# alignment: %s\n" % map_old2new.Write())
else:
map_old2new = None
for method in options.methods:
if method == "summary-numbers":
options.stdlog.write(
"""# Numbers of positive sites.
#
# The consistent row/column contains positive sites that are significant
# (above thresholds for probability and omega) for all models/analysis
# that have been selected (label: cons).
#
# The log-likelihood ratio test is performed for model pairs, depending
# on the output chosen.
# Significance threshold: %6.4f
# The pairs are 8 versus 7 and 2 versus 1 and 3 versus 0.
#
""" % options.significance_threshold )
# write header
if options.prefix:
options.stdout.write("prefix\t")
options.stdout.write("method\tnseq\t")
h = []
for model in options.models:
for analysis in options.analysis:
h.append("%s%s" % (analysis, model))
h.append("p%s" % (model))
h.append("df%s" % (model))
h.append("chi%s" % (model))
h.append("lrt%s" % (model))
options.stdout.write("\t".join(h))
options.stdout.write("\tcons\tpassed\tfilename\n")
nmethod = 0
consistent_cols = [None for x in range(len(options.analysis))]
passed_tests = {}
for m in options.models:
passed_tests[m] = 0
for result in results:
row_consistent = None
if options.prefix:
options.stdout.write("%s" % (options.prefix))
options.stdout.write("%i" % nmethod)
options.stdout.write("\t%i" % (result.mNumSequences))
npassed = 0
for model in options.models:
sites = result.mSites[model]
# do significance test
full_model, null_model = model, map_nested_models[model]
lrt = Stats.doLogLikelihoodTest(
result.mSites[full_model].mLogLikelihood,
result.mSites[full_model].mNumParameters,
result.mSites[null_model].mLogLikelihood,
result.mSites[null_model].mNumParameters,
options.significance_threshold)
x = 0
for analysis in options.analysis:
if analysis == "neb":
s = set(
map(extract_f, filter(filter_f, sites.mNEB.mPositiveSites)))
elif analysis == "beb":
s = set(
map(extract_f, filter(filter_f, sites.mBEB.mPositiveSites)))
options.stdout.write("\t%i" % (len(s)))
if not lrt.mPassed:
s = set()
if row_consistent is None:
row_consistent = s
else:
row_consistent = row_consistent.intersection(s)
if consistent_cols[x] is None:
consistent_cols[x] = s
else:
consistent_cols[x] = consistent_cols[
x].intersection(s)
x += 1
if lrt.mPassed:
c = "passed"
passed_tests[model] += 1
npassed += 1
else:
c = "failed"
options.stdout.write("\t%5.2e\t%i\t%5.2f\t%s" %
(lrt.mProbability,
lrt.mDegreesFreedom,
lrt.mChiSquaredValue,
c))
options.stdout.write(
"\t%i\t%i\t%s\n" % (len(row_consistent), npassed, headers[nmethod]))
nmethod += 1
if options.prefix:
options.stdout.write("%s\t" % options.prefix)
options.stdout.write("cons")
row_consistent = None
total_passed = 0
for model in options.models:
x = 0
for analysis in options.analysis:
s = consistent_cols[x]
if s is None:
s = set()
options.stdout.write("\t%i" % (len(s)))
if row_consistent is None:
row_consistent = s
else:
row_consistent = row_consistent.intersection(s)
x += 1
options.stdout.write("\tna\t%i" % passed_tests[model])
total_passed += passed_tests[model]
options.stdout.write(
"\t%i\t%i\n" % (len(row_consistent), total_passed))
elif method == "jalview":
options.stdout.write("JALVIEW_ANNOTATION\n")
options.stdout.write("# Created: %s\n\n" %
(time.asctime(time.localtime(time.time()))))
l = 1
x = 0
for result in results:
sites, significance = selectPositiveSites(
[result], options.selection_mode, options, mali)
codes = [""] * result.mLength
if len(sites) == 0:
continue
for site in sites:
codes[site - 1] = options.jalview_symbol
options.stdout.write(
"NO_GRAPH\t%s\t%s\n" % (options.jalview_titles[x], "|".join(codes)))
x += 1
elif method == "count-positive-sites":
sites, significance = selectPositiveSites(
results, options.selection_mode, options, mali)
options.stdout.write("%i\n" % (len(sites)))
elif method in ("positive-site-table", ):
sites, significance = selectPositiveSites(
results, options.selection_mode, options, mali)
headers = ["site", "P"]
if map_old2new:
headers.append("mapped")
headers.append("Pm")
options.stdout.write("\t".join(headers) + "\n")
sites = list(sites)
sites.sort()
nmapped, nunmapped = 0, 0
for site in sites:
values = [site, "%6.4f" % significance[site]]
if map_old2new:
r = map_old2new.mapRowToCol(site)
if r == 0:
values.append("na")
values.append("")
nunmapped += 1
if options.loglevel >= 2:
options.stdlog.write(
"# unmapped residue: %i\n" % site)
else:
values.append(r)
values.append(consensus[r - 1])
nmapped += 1
options.stdout.write("\t".join(map(str, (values))) + "\n")
if options.loglevel >= 1:
options.stdlog.write("# sites: ninput=%i, noutput=%i, nskipped=%i\n" % (
len(sites), nmapped, nunmapped))
E.info("ninput=%i, noutput=%i, nskipped=%i" % (ninput, noutput, nskipped))
E.Stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv == None: argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: sequences2mali.py 2782 2009-09-10 11:40:29Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-i",
"--input-format",
dest="input_format",
type="choice",
choices=("plain", "fasta", "clustal", "stockholm",
"phylip"),
help="input format of multiple alignment")
parser.add_option("-o",
"--output-format",
dest="output_format",
type="choice",
choices=("plain", "fasta", "stockholm", "phylip"),
help="output format of multiple alignment")
parser.add_option("-m",
"--method",
dest="method",
type="choice",
choices=("add", ),
help="""method to use to build multiple alignment.""")
parser.add_option("-p",
"--parameters",
dest="parameters",
type="string",
help="parameter stack for methods that require one.")
parser.add_option("-a",
"--alignment-method",
dest="alignment_method",
type="choice",
choices=("sw", "nw"),
help="alignment_method [%default].")
parser.set_defaults(
input_format="fasta",
output_format="fasta",
method=None,
parameters="",
gop=-10.0,
gep=-1.0,
alignment_method="sw",
)
(options, args) = E.Start(parser)
options.parameters = options.parameters.split(",")
iterator = FastaIterator.iterate(sys.stdin)
if options.method == "add":
mali = Mali.Mali()
mali.readFromFile(open(options.parameters[0], "r"),
format=options.input_format)
del options.parameters[0]
old_length = mali.getLength()
new_mali = convertMali2Mali(mali)
if options.alignment_method == "sw":
alignator = alignlib_lite.py_makeAlignatorFullDP(
options.gop, options.gep)
else:
alignator = alignlib_lite.py_makeAlignatorFullDPGlobal(
options.gop, options.gep)
while 1:
cur_record = iterator.next()
if cur_record is None: break
map_mali2seq = alignlib_lite.py_makeAlignataVector()
sequence = alignlib_lite.py_makeSequence(cur_record.sequence)
profile = alignlib_lite.py_makeProfileFromMali(new_mali)
if options.loglevel >= 4:
options.stdlog.write(profile.Write())
alignator.Align(profile, sequence, map_mali2seq)
if options.loglevel >= 3:
options.stdlog.write(map_mali2seq.Write())
## add sequence to mali
a = alignlib_lite.py_makeAlignatumFromString(cur_record.sequence)
a.thisown = 0
new_mali.addAlignatum(a, map_mali2seq, 1, 1, 1, 1, 1)
id = cur_record.title
mali.mIdentifiers.append(id)
mali.mMali[id] = Mali.AlignedString(
id, 0, len(cur_record.sequence),
new_mali.getRow(new_mali.getWidth() - 1).getString())
# substitute
for x in range(old_length):
mali.mMali[mali.mIdentifiers[x]].mString = new_mali.getRow(
x).getString()
mali.writeToFile(sys.stdout, format=options.output_format)
E.Stop()