def convertMali2Alignlib(mali):
'''convert a multiple alignment of type :class:`Mali`
into an alignlib_lite.py_multiple alignment object.
'''
import alignlib_lite
m = alignlib_lite.py_makeMultipleAlignment()
for identifier in mali.getIdentifiers():
a = alignlib_lite.py_makeAlignatum(mali[identifier])
m.add(a)
return m
def convertMali2Alignlib(mali):
'''convert a multiple alignment of type :class:`Mali`
into an alignlib_lite.py_multiple alignment object.
'''
import alignlib_lite
m = alignlib_lite.py_makeMultipleAlignment()
for identifier in mali.getIdentifiers():
a = alignlib_lite.py_makeAlignatum(mali[identifier])
m.add(a)
return m
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: peptides2cds.py 2890 2010-04-07 08:58:54Z andreas $")
parser.add_option("-p", "--peptides", dest="filename_peptides", type="string",
help="filename with peptide sequences [%default]." )
parser.add_option("-c", "--cds", "--cdnas", dest="filename_cdna", type="string",
help="filename with cdna sequences [%default]." )
parser.add_option("-m", "--map", dest="filename_map", type="string",
help="filename with map of peptide identifiers to cdna identifiers [%default]." )
parser.add_option( "--output-identifier", dest="output_identifier", type="choice",
choices=("cdna", "peptide"),
help="output identifier to use [%default]." )
parser.add_option("-f", "--output-format=", dest="output_format", type="choice",
choices=("alignment", "fasta"),
help="output format.")
parser.set_defaults(
peptides=None,
filename_cdna = None,
output_format="alignment",
filename_map = None,
stop_codons = ("TAG", "TAA", "TGA"),
output_identifier = "peptide",
)
(options, args) = E.Start( parser, add_pipe_options = True )
if not options.filename_cdna:
raise ValueError("please supply filename with cds sequences.")
if options.filename_peptides:
infile = open(options.filename_peptides, "r")
E.info("reading from %s" % options.filename_peptides)
else:
E.info("reading from stdin")
infile = sys.stdin
if options.filename_map:
E.info( "reading map" )
map_peptide2cds = IOTools.readMap( IOTools.openFile( options.filename_map, "r" ) )
E.info( "read map for %i identifiers" % len(map_peptide2cds) )
else:
map_peptide2cds = {}
E.info( "reading cds sequences" )
cds_sequences = Genomics.ReadPeptideSequences( IOTools.openFile(options.filename_cdna, "r") )
E.info( "read %i cds sequences" % len(cds_sequences))
ninput, noutput = 0, 0
nskipped, nnosequence = 0, 0
# iterate over peptide sequences
iterator = FastaIterator.FastaIterator( infile )
use_cds_id = options.output_identifier == "cds"
for cur_record in iterator:
ninput += 1
peptide_identifier = re.split("\s+", cur_record.title)[0]
cds_identifier = map_peptide2cds.get( peptide_identifier, peptide_identifier )
if cds_identifier not in cds_sequences:
nnosequence += 1
continue
p = cur_record.sequence
c = cds_sequences[cds_identifier]
E.debug("processing %s: laa=%i (without gaps=%i), lna=%i" % (peptide_identifier, len(p), len(re.sub("-", "", p)), len(c)))
try:
map_p2c = getMapPeptide2Cds( p, c, options )
except ValueError:
nskipped += 1
continue
if use_cds_id:
identifier = cds_identifier
else:
identifier = peptide_identifier
if options.output_format =="alignment":
options.stdout.write("\t".join( map(str, (identifier, alignlib_lite.py_AlignmentFormatEmissions( map_p2c ),
len(cur_record.sequence), len(cds_sequences[identifier])) ) )+"\n")
elif options.output_format == "fasta":
map_p2c.switchRowCol()
alignatum = alignlib_lite.py_makeAlignatum( c )
alignatum.mapOnAlignment( map_p2c, len(p) * 3 )
s = alignatum.getString()
if len(s) != len(p) * 3:
raise ValueError ("incomplete aligned string for %s: %s, cds=%s" % (cur_record.title, s, c ))
options.stdout.write( ">%s\n%s\n" % (identifier, s ))
noutput += 1
sys.stdout.flush()
E.info( "ninput=%i, noutput=%i, nnosequence=%i, nskipped=%i" % (ninput, noutput, nnosequence, 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: $Id$")
parser.add_option("-p",
"--peptides-fasta-file",
dest="filename_peptides",
type="string",
help="filename with peptide sequences [%default].")
parser.add_option("-c",
"--cds-gtf-file",
"--cdnas",
dest="filename_cdna",
type="string",
help="filename with cdna sequences [%default].")
parser.add_option(
"-m",
"--map",
dest="filename_map",
type="string",
help=
"filename with map of peptide identifiers to cdna identifiers [%default]."
)
parser.add_option("--output-identifier",
dest="output_identifier",
type="choice",
choices=("cdna", "peptide"),
help="output identifier to use [%default].")
parser.add_option("-f",
"--output-format=",
dest="output_format",
type="choice",
choices=("alignment", "fasta"),
help="output format.")
parser.set_defaults(
peptides=None,
filename_cdna=None,
output_format="alignment",
filename_map=None,
stop_codons=("TAG", "TAA", "TGA"),
output_identifier="peptide",
)
(options, args) = E.Start(parser, add_pipe_options=True)
if not options.filename_cdna:
raise ValueError("please supply filename with cds sequences.")
if options.filename_peptides:
infile = open(options.filename_peptides, "r")
E.info("reading from %s" % options.filename_peptides)
else:
E.info("reading from stdin")
infile = sys.stdin
if options.filename_map:
E.info("reading map")
map_peptide2cds = IOTools.readMap(
IOTools.openFile(options.filename_map, "r"))
E.info("read map for %i identifiers" % len(map_peptide2cds))
else:
map_peptide2cds = {}
E.info("reading cds sequences")
cds_sequences = Genomics.ReadPeptideSequences(
IOTools.openFile(options.filename_cdna, "r"))
E.info("read %i cds sequences" % len(cds_sequences))
ninput, noutput = 0, 0
nskipped, nnosequence = 0, 0
# iterate over peptide sequences
iterator = FastaIterator.FastaIterator(infile)
use_cds_id = options.output_identifier == "cds"
for cur_record in iterator:
ninput += 1
peptide_identifier = re.split("\s+", cur_record.title)[0]
cds_identifier = map_peptide2cds.get(peptide_identifier,
peptide_identifier)
if cds_identifier not in cds_sequences:
nnosequence += 1
continue
p = cur_record.sequence
c = cds_sequences[cds_identifier]
E.debug("processing %s: laa=%i (without gaps=%i), lna=%i" %
(peptide_identifier, len(p), len(re.sub("-", "", p)), len(c)))
try:
map_p2c = Peptides2Cds.getMapPeptide2Cds(p, c, options)
except ValueError:
nskipped += 1
continue
if use_cds_id:
identifier = cds_identifier
else:
identifier = peptide_identifier
if options.output_format == "alignment":
options.stdout.write("\t".join(
map(str, (identifier,
alignlib_lite.py_AlignmentFormatEmissions(map_p2c),
len(cur_record.sequence),
len(cds_sequences[identifier])))) + "\n")
elif options.output_format == "fasta":
map_p2c.switchRowCol()
alignatum = alignlib_lite.py_makeAlignatum(c)
alignatum.mapOnAlignment(map_p2c, len(p) * 3)
s = alignatum.getString()
if len(s) != len(p) * 3:
raise ValueError(
"incomplete aligned string for %s: %s, cds=%s" %
(cur_record.title, s, c))
options.stdout.write(">%s\n%s\n" % (identifier, s))
noutput += 1
sys.stdout.flush()
E.info("ninput=%i, noutput=%i, nnosequence=%i, nskipped=%i" %
(ninput, noutput, nnosequence, nskipped))
E.Stop()