#!/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 """ 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 <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 """ 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')