convertFormat.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Convert biosequences from one format to another.
Usage is: convbioseq [options] FORMAT INFILES ...
Options: 
--version show program's version number and exit 
-h, --help show this help message and exit 
-i FORMAT, --input-format=FORMAT 
The format of the input biosequence files. If not 
supplied, this will be inferred from the extension of 
the files. 
-e EXTENSION, --output-extension=EXTENSION 
The extension of the output biosequence files. If not 
supplied, this will be inferred from the output 
format.
And so for example:
convbioseq stockholm foo.genbank 
convbioseq -e fast fasta foo.aln 
convbioseq -i fasta phylip foo.txt
"""
# TODO: all the format crap should be in one table

__docformat__ = 'restructuredtext en'
__author__ = 'Paul-Michael Agapow <agapow@bbsrc.ac.uk>'


### IMPORTS ###

from os import path
from optparse import OptionParser
from exceptions import BaseException

from Bio import SeqIO

try:
   from bioscripts.convert import __version__
except:
   __version__ = 'unknown'
   

### CONSTANTS & DEFINES ###
# Formats in SeqIO that we don't parse as yet. There's no actual problem,
# these just need to be checked:
# ace embl fastq fastq-solex ig pir swiss tab qual

# what extensions to give for each output format
OUT_EXT_MAP = {
   'clustal': 'aln',
   'fasta': 'fasta',
   'genbank': 'gb', 
   'nexus': 'nexus',
   'phd': 'phd',
   'phylip': 'phy',
   'stockholm': 'sth',
   'qual': 'qual',
   'tab': 'tab',
}

# the list of known formats
KNOWN_FMTS = sorted (OUT_EXT_MAP.keys())

# what format to derive from inout extensions
# always accept the format name as an extension
IN_EXT_MAP = {
   'aln': 'clustal',
   'sth': 'stockholm',
   'gb': 'genbank',
   'nxs': 'nexus',
   'phy': 'phylip',
   'tab': 'tab',
   'qual': 'qual',
   'phd': 'phd',
}
IN_EXT_MAP.update (dict ([(x, x) for x in KNOWN_FMTS]))

_DEV_MODE = True


### IMPLEMENTATION ###

def parse_args():
   # Construct the option parser.
   usage = '%prog [options] FORMAT INFILES ...'
   version = "version %s" %  __version__  
   epilog='FORMAT must be one of %s.\n' % ', '.join (["'%s'" % x for x in
      KNOWN_FMTS])
   epilog += 'The input formats inferred from extensions are %s.\n' % \
      ', '.join (["%s ('.%s')" % (v, k) for k, v in IN_EXT_MAP.iteritems()])
   epilog += 'The default extensions for output formats are %s.\n' % \
         ', '.join (["'.%s' (%s)" % (v, k) for k, v in OUT_EXT_MAP.iteritems()])
   optparser = OptionParser (usage=usage, version=version, epilog=epilog)
   
   optparser.add_option ('--input-format', '-i',
       dest="input_format",
       help='''The format of the input biosequence files. If not supplied, this will be inferred from the extension of the files.''',
      metavar='FORMAT',
   )
         
   optparser.add_option ('--output-extension', '-e',
       dest="output_extension",
       help='''The extension of the output biosequence files. If not supplied, this will be inferred from the output format.''',
      metavar='EXTENSION',
   )
         
   #optparser.add_option ('--verbose', '-v',
   #   dest="verbose",
   #   help='''How much output to generate.''')
         
   options, pargs = optparser.parse_args()
   
   if (len (pargs) < 1):
      optparser.error ('No output format specified')
   out_fmt = pargs[0].lower()
   assert (out_fmt in KNOWN_FMTS), "unknown output format"
   infiles = pargs[1:]
   if (not infiles):
      optparser.error ('No input files specified')
   
   return out_fmt, infiles, options


def main():
   out_fmt, infiles, options = parse_args()
   
   for in_path in infiles:
      # construct parameters
      dir_name, file_name = path.split (in_path) 
      base_name, orig_ext = path.splitext (file_name)
      if (orig_ext.startswith ('.')):
         orig_ext = orig_ext[1:]
      in_fmt = (options.input_format or IN_EXT_MAP.get (orig_ext, '')).lower()
      assert (in_fmt), "no known input format specified"
      out_ext = options.output_extension or OUT_EXT_MAP[out_fmt]
      out_path = path.join (dir_name, '%s.%s' % (base_name, out_ext))
      # open files
      in_hndl = open (in_path, 'rb')
      out_hndl = open (out_path, 'wb')
      # read and write
      in_seqs = [x for x in SeqIO.parse (in_hndl, in_fmt)]
      assert (in_seqs), '''No sequences read from %s. Perhaps the file is not in %s format.''' % (file_name, in_fmt)
      SeqIO.write (in_seqs, out_hndl, out_fmt)
      # tidy up
      in_hndl.close()
      out_hndl.close()
   
   
### TEST & DEBUG ###

### MAIN ###

if __name__ == '__main__':
   try:
      main()
   except BaseException, err:
      if (_DEV_MODE):
         raise
      else:
         print err
   except:
      print "An unknown error occurred.\n"
         
         

   
   

### END ######################################################################