def run(self):
"""
"""
if self.debug:
import pdb
pdb.set_trace()
if not os.path.isfile(self.inputFname):
sys.stderr.write("Error: file, %s, is not a file.\n" %
(self.inputFname))
sys.exit(3)
inputFile = utils.openGzipFile(self.inputFname, 'r')
outputPolymorphismFile = PolymorphismTableFile(self.outputFname, openMode='w', isPhased=1, \
ploidy=self.ploidy)
outputChromosomeSequenceFile = open(self.outputChromosomeSequenceFname,
"w")
commandline = inputFile.next().strip()
outputPolymorphismFile.addAttribute('commandline',
value=commandline,
overwrite=True,
tableName='polymorphism')
for line in inputFile:
if self.iterationPattern.search(
line): #one iteration is regarded as one species
self.outputOneIteration(inputFile=inputFile, iterationLine=line, outputPolymorphismFile=outputPolymorphismFile,\
outputChromosomeSequenceFile=outputChromosomeSequenceFile, ploidy=self.ploidy)
inputFile.close()
outputPolymorphismFile.close()
outputChromosomeSequenceFile.close()
def run(self):
"""
input looks like (inputFileFormat=1)
msHOT-lite 2 1 -t 4781.50413187402 -r 790.4466018 ...
//
segsites: 40567
positions: 0.0002 0.0003
001001101011011001...
101001010100101111...
...
./msHOT-lite 2 1 -t 84989.8346003745 -r 34490.1412746802 30000000 -l -en 0.0013 1 0.0670 -en 0.0022 1 0.3866 -en 0.0032 1 0.3446 -en 0.0044 1 0.21
79 -en 0.0059 1 0.1513 -en 0.0076 1 0.1144 -en 0.0096 1 0.0910 -en 0.0121 1 0.0757 -en 0.0150 1 0.0662 -en 0.0184 1 0.0609 -en 0.0226 1 0.0583 -en
0.0275 1 0.0572 -en 0.0333 1 0.0571 -en 0.0402 1 0.0577 -en 0.0485 1 0.0589 -en 0.0583 1 0.0603 -en 0.0700 1 0.0615 -en 0.0839 1 0.0624 -en 0.100
5 1 0.0632 -en 0.1202 1 0.0641 -en 0.1437 1 0.0651 -en 0.1716 1 0.0663 -en 0.2048 1 0.0678 -en 0.2444 1 0.0696 -en 0.2914 1 0.0719 -en 0.3475 1 0.
0752 -en 0.4935 1 0.0794
//
@begin 6422
30000000
1100 01
6074 10
29966899 10
29971027 01
29973740 01
29982767 01
29985696 10
@end
"""
if self.debug:
import pdb
pdb.set_trace()
if not os.path.isfile(self.inputFname):
sys.stderr.write("Error: file, %s, is not a file.\n" %
(self.inputFname))
sys.exit(3)
inputFile = utils.openGzipFile(self.inputFname, 'r')
outputPolymorphismFile = PolymorphismTableFile(self.outputFname, openMode='w', isPhased=1, \
ploidy=self.ploidy)
commandline = inputFile.next().strip()
outputPolymorphismFile.addAttribute('commandline',
value=commandline,
overwrite=True,
tableName='polymorphism')
self._convert(inputFile=inputFile,
outputPolymorphismFile=outputPolymorphismFile,
ploidy=self.ploidy)
inputFile.close()
outputPolymorphismFile.close()