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):
if argv is None:
argv = sys.argv
parser = E.OptionParser(
version=
"%prog version: $Id: align_all_vs_all.py 2782 2009-09-10 11:40:29Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-s",
"--sequences",
dest="filename_sequences",
type="string",
help="input file with sequences")
parser.set_defaults(
filename_sequences=None,
gop=-10.0,
gep=-1.0,
)
(options, args) = E.Start(parser, add_pipe_options=True)
if options.filename_sequences:
infile = open(options.filename_sequences, "r")
else:
infile = sys.stdin
parser = FastaIterator.FastaIterator(infile)
sequences = []
while 1:
cur_record = iterator.next()
if cur_record is None:
break
sequences.append(
(cur_record.title,
alignlib_lite.py_makeSequence(re.sub(" ", "",
cur_record.sequence))))
if options.filename_sequences:
infile.close()
alignator = alignlib_lite.py_makeAlignatorFullDP(options.gop, options.gep)
map_a2b = alignlib_lite.py_makeAlignataVector()
nsequences = len(sequences)
for x in range(0, nsequences - 1):
for y in range(x + 1, nsequences):
alignator.Align(sequences[x][1], sequences[y][1], map_a2b)
row_ali, col_ali = alignlib_lite.py_writeAlignataCompressed(
map_a2b)
options.stdout.write(
"%s\t%s\t%i\t%i\t%i\t%s\t%i\t%i\t%s\t%i\t%i\t%i\t%i\n" %
(sequences[x][0], sequences[y][0], map_a2b.getScore(),
map_a2b.getRowFrom(), map_a2b.getRowTo(), row_ali,
map_a2b.getColFrom(), map_a2b.getColTo(), col_ali,
map_a2b.getScore(),
100 * alignlib_lite.py_calculatePercentIdentity(
map_a2b, sequences[x][1], sequences[y][1]),
sequences[x][1].getLength(), sequences[y][1].getLength()))
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()
def main( argv = None ):
if argv == None: argv = sys.argv
parser = E.OptionParser( version = "%prog version: $Id: align_all_vs_all.py 2782 2009-09-10 11:40:29Z andreas $",
usage = globals()["__doc__"] )
parser.add_option("-s", "--sequences", dest="filename_sequences", type="string",
help="input file with sequences" )
parser.set_defaults(
filename_sequences = None,
gop = -10.0,
gep = -1.0,
)
(options, args) = E.Start( parser, add_pipe_options = True )
if options.filename_sequences:
infile = open(options.filename_sequences, "r")
else:
infile = sys.stdin
parser = FastaIterator.FastaIterator( infile )
sequences = []
while 1:
cur_record = iterator.next()
if cur_record is None: break
sequences.append( (cur_record.title, alignlib_lite.py_makeSequence(re.sub( " ", "", cur_record.sequence)) ) )
if options.filename_sequences:
infile.close()
alignator = alignlib_lite.py_makeAlignatorFullDP( options.gop, options.gep )
map_a2b = alignlib_lite.py_makeAlignataVector()
nsequences = len(sequences)
for x in range(0,nsequences-1):
for y in range(x+1, nsequences):
alignator.Align( sequences[x][1], sequences[y][1], map_a2b)
row_ali, col_ali = alignlib_lite.py_writeAlignataCompressed( map_a2b )
options.stdout.write( "%s\t%s\t%i\t%i\t%i\t%s\t%i\t%i\t%s\t%i\t%i\t%i\t%i\n" % (\
sequences[x][0], sequences[y][0],
map_a2b.getScore(),
map_a2b.getRowFrom(),
map_a2b.getRowTo(),
row_ali,
map_a2b.getColFrom(),
map_a2b.getColTo(),
col_ali,
map_a2b.getScore(),
100 * alignlib_lite.py_calculatePercentIdentity( map_a2b, sequences[x][1], sequences[y][1]),
sequences[x][1].getLength(),
sequences[y][1].getLength() ))
E.Stop()
