def MapRange(self, query_token, query_from, query_to):
"""map something."""
map_query2sbjct = alignlib_lite.py_makeAlignataVector()
alignlib_lite.py_fillAlignataCompressed(map_query2sbjct,
self.mQueryFrom, self.mQueryAli,
self.mSbjctFrom, self.mSbjctAli)
new_from = 0
if query_from <= map_query2sbjct.getRowTo():
x = max(query_from, self.mQueryFrom)
while map_query2sbjct.mapRowToCol(x) == 0:
x += 1
if x > map_query2sbjct.getRowTo():
break
else:
new_from = map_query2sbjct.mapRowToCol(x)
new_to = 0
if query_to >= map_query2sbjct.getRowFrom():
x = min(query_to, self.mQueryTo)
while map_query2sbjct.mapRowToCol(x) == 0:
x -= 1
if x < map_query2sbjct.getRowFrom():
break
else:
new_to = map_query2sbjct.mapRowToCol(x)
return self.mSbjctToken, new_from, new_to
def Expand(self):
if not self.mIsExpanded:
self.mMapQuery2Sbjct = alignlib_lite.py_makeAlignataVector()
alignlib_lite.py_fillAlignataCompressed(self.mMapQuery2Sbjct,
self.mQueryFrom, self.mQueryAli,
self.mSbjctFrom, self.mSbjctAli)
self.mIsExpanded = True
def MapRange(self, query_token, query_from, query_to):
"""map something."""
map_query2sbjct = alignlib_lite.py_makeAlignataVector()
alignlib_lite.py_fillAlignataCompressed(map_query2sbjct,
self.mQueryFrom, self.mQueryAli,
self.mSbjctFrom, self.mSbjctAli)
new_from = 0
if query_from <= map_query2sbjct.getRowTo():
x = max(query_from, self.mQueryFrom)
while map_query2sbjct.mapRowToCol(x) == 0:
x += 1
if x > map_query2sbjct.getRowTo():
break
else:
new_from = map_query2sbjct.mapRowToCol(x)
new_to = 0
if query_to >= map_query2sbjct.getRowFrom():
x = min(query_to, self.mQueryTo)
while map_query2sbjct.mapRowToCol(x) == 0:
x -= 1
if x < map_query2sbjct.getRowFrom():
break
else:
new_to = map_query2sbjct.mapRowToCol(x)
return self.mSbjctToken, new_from, new_to
def Expand(self):
if not self.mIsExpanded:
self.mMapQuery2Sbjct = alignlib_lite.py_makeAlignataVector()
alignlib_lite.py_fillAlignataCompressed(self.mMapQuery2Sbjct,
self.mQueryFrom, self.mQueryAli,
self.mSbjctFrom, self.mSbjctAli)
self.mIsExpanded = True
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: blast2fasta.py 2782 2009-09-10 11:40:29Z andreas $",
usage = globals()["__doc__"] )
parser.add_option("-s", "--sequences", dest="filename_sequences", type="string",
help="filename with sequences." )
parser.add_option("-f", "--format", dest="format", type="string",
help="output format." )
parser.set_defaults(
filename_sequences = None,
format = "fasta",
)
(options, args) = E.Start( parser )
if not options.filename_sequences:
raise "please supply filename with sequences."
sequences = Genomics.ReadPeptideSequences( open(options.filename_sequences, "r") )
if options.loglevel >= 1:
print "# read %i sequences" % len(sequences)
for k in sequences.keys():
sequences[k] = alignlib_lite.py_makeSequence( sequences[k] )
if options.loglevel >= 2:
print "# converted %i sequences" % len(sequences)
ninput, noutput, nskipped, nfailed = 0, 0, 0, 0
link = BlastAlignments.Link()
ali = alignlib_lite.py_makeAlignataVector()
for line in sys.stdin:
if line[0] == "#": continue
link.Read( line )
ninput += 1
if link.mQueryToken not in sequences or link.mSbjctToken not in sequences:
nskipped += 1
continue
ali.Clear()
alignlib_lite.py_fillAlignataCompressed( ali, link.mQueryFrom, link.mQueryAli, link.mSbjctFrom, link.mSbjctAli )
result = alignlib_lite.py_writePairAlignment( sequences[link.mQueryToken], sequences[link.mSbjctToken], ali ).split("\n")
if len(result) != 3:
nfailed += 1
if options.format == "fasta":
print ">%s %i-%i\n%s\n>%s %i-%i\n%s\n" %\
(link.mQueryToken, link.mQueryFrom, link.mQueryTo, result[0].split("\t")[1],
link.mSbjctToken, link.mSbjctFrom, link.mSbjctTo, result[1].split("\t")[1] )
noutput += 1
E.info( "ninput=%i, noutput=%i, nskipped=%i, nfailed=%i" % (ninput, noutput, nskipped, nfailed) )
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: blast2fasta.py 2782 2009-09-10 11:40:29Z andreas $",
usage=globals()["__doc__"])
parser.add_option("-s",
"--sequences",
dest="filename_sequences",
type="string",
help="filename with sequences.")
parser.add_option("-f",
"--format",
dest="format",
type="string",
help="output format.")
parser.set_defaults(
filename_sequences=None,
format="fasta",
)
(options, args) = E.Start(parser)
if not options.filename_sequences:
raise "please supply filename with sequences."
sequences = Genomics.ReadPeptideSequences(
open(options.filename_sequences, "r"))
if options.loglevel >= 1:
print "# read %i sequences" % len(sequences)
for k in sequences.keys():
sequences[k] = alignlib_lite.py_makeSequence(sequences[k])
if options.loglevel >= 2:
print "# converted %i sequences" % len(sequences)
ninput, noutput, nskipped, nfailed = 0, 0, 0, 0
link = BlastAlignments.Link()
ali = alignlib_lite.py_makeAlignataVector()
for line in sys.stdin:
if line[0] == "#": continue
link.Read(line)
ninput += 1
if link.mQueryToken not in sequences or link.mSbjctToken not in sequences:
nskipped += 1
continue
ali.Clear()
alignlib_lite.py_fillAlignataCompressed(ali, link.mQueryFrom,
link.mQueryAli,
link.mSbjctFrom,
link.mSbjctAli)
result = alignlib_lite.py_writePairAlignment(
sequences[link.mQueryToken], sequences[link.mSbjctToken],
ali).split("\n")
if len(result) != 3:
nfailed += 1
if options.format == "fasta":
print ">%s %i-%i\n%s\n>%s %i-%i\n%s\n" %\
(link.mQueryToken, link.mQueryFrom, link.mQueryTo, result[0].split("\t")[1],
link.mSbjctToken, link.mSbjctFrom, link.mSbjctTo, result[1].split("\t")[1] )
noutput += 1
E.info("ninput=%i, noutput=%i, nskipped=%i, nfailed=%i" %
(ninput, noutput, nskipped, nfailed))
E.Stop()
