Python Alignment.load 예제들

예제 #1

파일: fasta2clustal.py 프로젝트: SiriusShiu/Mungo

#!/usr/bin/env python

"""
fasta2clustal.py <input filename> <output filename>

Author: Tony Papenfuss
Date: Thu Jun  7 17:58:39 EST 2007

"""

import os, sys
from optparse import OptionParser
from mungo.align import Alignment


usage = "%prog [options] <input file> <output file>"
parser = OptionParser(usage=usage)
options, args = parser.parse_args(sys.argv)

if len(args) != 3:
    sys.exit(__doc__)

iFilename = args[1]
oFilename = args[2]

alignment = Alignment.load(iFilename, format="fasta")
alignment.save(oFilename, format="clustal")

예제 #2

#!/usr/bin/env python
"""
fasta2nexus.py

Author: Tony Papenfuss
Date: Wed May  9 17:23:18 EST 2007

"""

import os, sys
from mungo.align import Alignment

aln = Alignment.load(sys.argv[1], format='fasta')
aln.save(sys.argv[2], format='nexus')

예제 #3

#!/usr/bin/env python
"""
clustal2nexus.py <input file> <output file>
"""

import sys
from optparse import OptionParser
from mungo.align import Alignment

usage = "%prog [options] <input file> <output file>"
parser = OptionParser(usage=usage)
options, args = parser.parse_args(sys.argv)

if len(args) != 3:
    sys.exit(__doc__)

aln = Alignment.load(args[1], format='clustal')
aln.save(args[2], format='nexus')

예제 #4

파일: fasta2clustal.py 프로젝트: PapenfussLab/Mungo

#!/usr/bin/env python
"""
fasta2clustal.py <input filename> <output filename>

Author: Tony Papenfuss
Date: Thu Jun  7 17:58:39 EST 2007

"""

import os, sys
from optparse import OptionParser
from mungo.align import Alignment

usage = "%prog [options] <input file> <output file>"
parser = OptionParser(usage=usage)
options, args = parser.parse_args(sys.argv)

if len(args) != 3:
    sys.exit(__doc__)

iFilename = args[1]
oFilename = args[2]

alignment = Alignment.load(iFilename, format='fasta')
alignment.save(oFilename, format='clustal')

예제 #5

파일: fasta2phylip.py 프로젝트: SiriusShiu/Mungo

#!/usr/bin/env python

"""
clustal2phylip.py <input filename> <output filename>

Author: Tony Papenfuss
Date: Mon Jan  8 11:44:37 EST 2007

"""

import os, sys
from optparse import OptionParser
from mungo.align import Alignment


usage = "%prog [options] <input file> <output file>"
parser = OptionParser(usage=usage)
options, args = parser.parse_args(sys.argv)

if len(args)!=3:
    sys.exit(__doc__)

iFilename = args[1]
oFilename = args[2]

alignment = Alignment.load(iFilename, format='fasta')
alignment.save(oFilename, format='phylip')

예제 #6

파일: clustal2nexus.py 프로젝트: SiriusShiu/Mungo

#!/usr/bin/env python

"""
clustal2nexus.py <input file> <output file>
"""

import sys
from optparse import OptionParser
from mungo.align import Alignment


usage = "%prog [options] <input file> <output file>"
parser = OptionParser(usage=usage)
options, args = parser.parse_args(sys.argv)

if len(args)!=3:
    sys.exit(__doc__)

aln = Alignment.load(args[1], format='clustal')
aln.save(args[2], format='nexus')

예제 #7

파일: fasta2nexus.py 프로젝트: SiriusShiu/Mungo

#!/usr/bin/env python

"""
fasta2nexus.py

Author: Tony Papenfuss
Date: Wed May  9 17:23:18 EST 2007

"""

import os, sys
from mungo.align import Alignment


aln = Alignment.load(sys.argv[1], format='fasta')
aln.save(sys.argv[2], format='nexus')