def convertMali2Mali(mali):
"""convert a mali to a profile."""
new_mali = alignlib_lite.py_makeMultipleAlignment()
for id in mali.getIdentifiers():
s = alignlib_lite.py_makeAlignatumFromString(mali[id])
s.thisown = 0
new_mali.addAlignatum(s)
return new_mali
def convertMali2Mali(mali):
"""convert a mali to a profile."""
new_mali = alignlib_lite.py_makeMultipleAlignment()
for id in mali.getIdentifiers():
s = alignlib_lite.py_makeAlignatumFromString(mali[id])
s.thisown = 0
new_mali.addAlignatum(s)
return new_mali
def readPicasso(infile):
"""read alignment in the non-defined picasso format.
"""
mali = alignlib_lite.py_makeMultipleAlignment()
while 1:
line = infile.readline()
if not line: break
x = re.search("\d+\s+([A-Z\-\.]*)\s+\d+", line)
if x:
s = x.groups()[0]
a = alignlib_lite.py_makeAlignatumFromString(s)
a.thisown = 0
mali.addAlignatum(a)
return mali
def readPicasso( infile ):
"""read alignment in the non-defined picasso format.
"""
mali = alignlib_lite.py_makeMultipleAlignment()
while 1:
line = infile.readline()
if not line: break
x = re.search( "\d+\s+([A-Z\-\.]*)\s+\d+", line)
if x:
s = x.groups()[0]
a = alignlib_lite.py_makeAlignatumFromString(s)
a.thisown = 0
mali.addAlignatum( a )
return mali
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 == 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()
