#!/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')
#!/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')
#!/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")
#!/usr/bin/env python
"""
clustal2phylip.py [-w width] <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 [-w width] <input file> <output file>"
parser = OptionParser(usage=usage)
parser.add_option('-w', '--width', dest='width', action='store',
type='int', default=10, help='Name field width')
options, args = parser.parse_args(sys.argv)
iFilename = args[1]
oFilename = args[2]
alignment = Alignment.loadClustal(iFilename)
alignment.save(oFilename, format='phylip', width=options.width)
#!/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')
#!/usr/bin/env python
"""
stockholm2fasta.py <stockholm filename> <fasta filename>
Author: Tony Papenfuss
Date: Sun May 6 13:34 EST 2007
"""
import os, sys
from mungo.align import Alignment
iFilename = sys.argv[1]
oFilename = sys.argv[2]
alignment = Alignment.loadStockholm(iFilename)
for name in alignment:
alignment[name] = alignment[name].replace('.', '-')
alignment.saveFasta(oFilename)
#!/usr/bin/env python """ clustal2molphy.py Author: Tony Papenfuss Date: Mon Mar 19 16:56:44 EST 2007 """ import os, sys from mungo.align import Alignment alignment = Alignment.loadClustal(sys.argv[1]) alignment.saveMolphy(sys.argv[2])
#!/usr/bin/env python
"""
clustal2noninterleaved.py <input file> <output file>
Author: Tony Papenfuss
Date: Fri May 11 23:33:06 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__)
aln = Alignment.loadClustal(args[1])
aln.saveClustal(args[2], interleaved=False)
#!/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')
#!/usr/bin/env python
"""
clustal2fasta.py <input file> <output file>
"""
import sys
from optparse import OptionParser
from mungo.align import Alignment
from mungo.fasta import FastaWriter
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.loadClustal(args[1])
writer = FastaWriter(args[2])
for name in aln:
writer.write(name, aln[name])
writer.close()
#!/usr/bin/env python
"""
clustal2phylip.py [-w width] <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 [-w width] <input file> <output file>"
parser = OptionParser(usage=usage)
parser.add_option('-w',
'--width',
dest='width',
action='store',
type='int',
default=10,
help='Name field width')
options, args = parser.parse_args(sys.argv)
iFilename = args[1]
oFilename = args[2]
alignment = Alignment.loadClustal(iFilename)
alignment.save(oFilename, format='phylip', width=options.width)
#!/usr/bin/env python
"""
stockholm2clustal.py <stockholm filename> <clustal filename>
Author: Tony Papenfuss
Date: Sun May 6 13:34 EST 2007
"""
import os, sys
from mungo.align import Alignment
iFilename = sys.argv[1]
oFilename = sys.argv[2]
alignment = Alignment.loadStockholm(iFilename)
for name in alignment:
alignment[name] = alignment[name].replace(".", "-")
alignment.saveClustal(oFilename)
#!/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')
#!/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')