create_newcazy_dictionary_with_subfamilies.py

#!/usr/bin/python
# File created on 13 Feb 2014.

# Author = "Erick Cardenas Poire"

import pickle
import sys
import Bio
from Bio import SeqIO
import re
from optparse import OptionParser

#config = load_config()
script_info={}
script_info['brief_description'] = """ This script will parse the CAZy database 
             file and generate a dictionary that will be stored as a pickle object"""

script_info['script_usage'] = []

usage = '''
Usage:  
python ./create_newcazy_dictionary_with_subfamilies  -i <input proteins>  -o <output_dictionary.pkl>


DEPENDENCIES: 	i)Biopython
'''

parser = OptionParser(usage)
parser.add_option("-i", "--input_fasta", dest = "input_file",
                  help = 'The input fasta protein [REQUIRED]')
parser.add_option("-o", "--output_pickle", dest = "output_file",
                  help = 'The output file [REQUIRED]')

# checks if the supplied arguments are adequate
def valid_arguments(opts, args):
    if (opts.input_file == None or opts.output_file == None ):
        return True
    else:
        return False


def main(argv):
    (opts, args) = parser.parse_args()
    print ''
    print 'Initializing...'

    if valid_arguments(opts, args):
        print usage
        sys.exit(0)

    # initialize the input directory or file
    input_file = opts.input_file 
    output_file = opts.output_file 
    filein = open(input_file,'rb')
    fileout = open(output_file,'w')

    cazydict = {}
    counter = 0
    for seq_record in SeqIO.parse(filein, format = "fasta"):
        description = seq_record.description
#        print seq_record.id
        subject = seq_record.name
        # Capture organism information
        organismsearch = re.search('(\[)([A-Za-z0-9\.\_\-\s\'\/\=\#\(\)\:\*\&]+)(\])', description)
        if organismsearch == None:
            organism = "None"
        else:
            organism = organismsearch.group(0)
            organism = organism.strip('[]')

        # Capture CAZy family information
        #description_search = re.search('(\()(CAZy)(\:)([AGCP])([AHTEL])(\:)([A-Z0-9_:]+)(\))', description)
        description_search = re.search('(\()([CAZY]+)(\:)([A-Z0-9\_\:]+)(\)) ', description)
        description_search = re.search('(\()([CAZy]+)(\:)([0-9A-Za-z\_\:\[\],]+)(\))', description)
#        print description

        if description_search == None:
            print 'No CAZY family found for:'
            print description


        familydata = description_search.group(0)
        the_cazy_class = familydata.split(':')
#        print familydata
        cazy_class = the_cazy_class[1].strip(' (')
        cazy_family = the_cazy_class[2].strip(')')
        cazy_subfamily = the_cazy_class[3].strip(')')
        if cazy_subfamily.find('[') != -1:
            print 'I found some weird results'
            print description
            print 'Setting subfamily to none'
            cazy_subfamily = 'none'

        # Create empty list to append the results 
        result = []
        result.append(description)
        result.append(cazy_family)
        result.append(cazy_class)
        result.append(cazy_subfamily)
        result.append(organism)

        # Update dictionary with results
        cazydict[subject] = result
        counter = counter + 1
        text = "\r   Sequences found : %s" %counter
        sys.stderr.write(text)
        sys.stderr.flush()
    print ''
    print 'writing to %s' %output_file
    pickle.dump(cazydict,fileout)


# Run main function 
main(sys.argv[1:])