A single-use script for cleaning up taxonomy strings from a nifH database generated by Gady and Buckley (2012) and exported by the authors from ARB. This is being use to hack together a 13_5 release of a nifH database for use with PrimerProspector and QIIME. The database reference is: PLoS One. 2012;7(7):e42149. doi: 10.1371/journal.pone.0042149…

clean_nifH_tax.py

#!/usr/bin/env python
# File created on 07 May 2013
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.6.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "[email protected]"
__status__ = "Development"

from collections import defaultdict
from qiime.util import parse_command_line_parameters, make_option

script_info = {}
script_info['brief_description'] = ""
script_info['script_description'] = ""
script_info['script_usage'] = [("","","")]
script_info['output_description']= ""
script_info['required_options'] = [
 make_option('-i','--input_fp',type="existing_filepath",help='the input filepath'),
 make_option('-o','--output_fp',type="new_filepath",help='the output filepath'),
]
script_info['optional_options'] = []
script_info['version'] = __version__



def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)

    f = open(opts.input_fp,'U')
    g = open(opts.output_fp,'w')
    l1 = defaultdict(int)
    l2 = defaultdict(int)
    for line in f:
        fields = line.strip().split('\t')
        id_ = fields[0]
        try:
            tax = fields[1]
        except IndexError:
            tax = 'Unclassified;Unclassified'
            l1['Unclassified'] += 1
            l2['Unclassified'] += 1
        else:
            tax = tax.split('/')
            if len(tax) == 1 and tax[0].startswith('Species'):
                tax = 'Unclassified;Unclassified'
                l1['Unclassified'] += 1
                l2['Unclassified'] += 1
            elif len(tax) == 1:
                l1[tax[0]] += 1
                l2['Unclassified'] += 1
                tax = '%s;Unclassified' % tax[0]
            elif len(tax) != 2:
                raise ValueError, "Bad number of fields: %s" % repr(tax)
            elif tax[1] == 'IA':
                l1['%s/IA' % tax[0]] += 1
                l2['Unclassified'] += 1
                tax = '%s/IA;Unclassified' % tax[0]
            else:
                l1[tax[0]] += 1
                l2[tax[1]] += 1
                tax = ';'.join(tax)
        g.write('%s\t%s\n' % (id_,tax))
    g.close()
    
    total_l1 = 0
    print "L1 summary"
    print "=========="
    for k, v in l1.items():
        print k, v
        total_l1 += v
    print "Total L1: ", total_l1
    print ""
    
    total_l2 = 0
    print "L2 summary"
    print "=========="
    for k, v in l2.items():
        print k, v
        total_l2 += v
    print "Total L2: ", total_l2
    print ""
        

if __name__ == "__main__":
    main()