def __init__(self):
Predictor.__init__(self)
self.mParser = PredictionParser.PredictionParserExonerate()
self.mParser.SetRestrictToStrand("+")
self.mExecutable = "exonerate"
self.mOptions = "-Q protein -T dna -m p2g --softmasktarget TRUE --forcegtag TRUE --forwardcoordinates FALSE"
self.mOutputOptions = '--showalignment FALSE --showvulgar FALSE --showsugar FALSE --showcigar FALSE ' + \
' --ryo "diy\t%S\t%ql\t%r\t%pi\t%ps\t%V\n" --showtargetgff FALSE --showquerygff FALSE'
def Run(self, peptide_sequence, genomic_sequence):
self.CreateTemporaryFiles()
outfile = open(self.mFilenameTempPeptide, "w")
outfile.write(">%s\n%s\n" % ("peptide", peptide_sequence))
outfile.close()
outfile = open(self.mFilenameTempGenome, "w")
outfile.write(">%s\n%s\n" % ("genome", genomic_sequence))
outfile.close()
statement = string.join(
map(str, (
self.mExecutable,
self.mDefaultOptions,
self.mOptions,
self.mOutputOptions,
"--query",
self.mFilenameTempPeptide,
"--target",
self.mFilenameTempGenome,
)), " ")
if self.mLogLevel >= 3:
print "# statement: %s" % statement
s = subprocess.Popen(statement,
shell=True,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
cwd=self.mTempDirectory,
close_fds=True)
(out, err) = s.communicate()
if s.returncode != 0:
raise ExonerateError, "Error in calculating Exonerate\n%s" % err
self.mStdout.write(out)
self.mStderr.write(err)
self.DeleteTemporaryFiles()
parser = PredictionParser.PredictionParserExonerate()
if self.mDoParse:
return parser.Parse(out, peptide_sequence, genomic_sequence)
# read peptide sequences
if param_filename_peptides:
peptide_sequences = Genomics.ReadPeptideSequences(
open(param_filename_peptides, "r"))
else:
peptide_sequences = {}
# print HEADER
if param_loglevel >= 2:
print SHORT_HEADER_SUMMARY
# aligned entries from exonerate
entries = []
parser = PredictionParser.PredictionParserExonerate()
if param_format == "exonerate":
for line in sys.stdin:
if line[0] == "#":
continue
if line[:3] != "diy":
continue
data = string.split(line[:-1], "\t")
query_token = data[1]
# parser has to go inside, because GetBestMatch returns reference
# copy
