Script for summarizing barcode error in the 'ultra-deep' ANL sequencing run

summarize_barcodes.py

#!/usr/bin/env python
# File created on 03 Jul 2012
from __future__ import division

__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME project"
__credits__ = ["Greg Caporaso"]
__license__ = "GPL"
__version__ = "1.5.0-dev"
__maintainer__ = "Greg Caporaso"
__email__ = "gregcaporaso@gmail.com"
__status__ = "Development"
 

from glob import glob
from os.path import split, join
from qiime.golay import decode
from qiime.parse import MinimalFastqParser
from qiime.util import parse_command_line_parameters, make_option, gzip_open

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_glob',help='wildcard string to match input barcode file(s)'),
 make_option('-o','--output_dir',type="new_dirpath",help='the output directory'),
 make_option('-b','--correct_barcode',help="the expected barcode sequence")
]
script_info['optional_options'] = []
script_info['version'] = __version__




def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)
    correct_barcode = opts.correct_barcode
    results = {}
    fps = glob("%s" % opts.input_glob)
    for fp in fps:
        lane_id = split(fp)[1].split('_')[0]
        for _, seq, _ in MinimalFastqParser(gzip_open(fp)):
            try:
                results[seq] += 1
            except KeyError:
                results[seq] = 1
    
    all_f = open(join(opts.output_dir,'barcode_counts.txt'),'w')
    summary_f = open(join(opts.output_dir,'result_summary.txt'),'w')
    summary_f.write('# %s\n' % ' '.join(fps))
    
    data = [(v,k) for k, v in results.items()]
    data.sort()
    summary = {}
    summary[True] = {0:0,1:0,2:0,3:0,4:0,-1:0}
    summary[False] = {0:0,1:0,2:0,3:0,4:0,-1:0}
    
    for count,bc in data[::-1]:
        try:
            new, diffs = decode(bc)
        except KeyError:
            new, diffs = "Can't decode", -1
        all_f.write('%s\t%s\t%d\t%d\t%s\t%s\n' % (lane_id,bc,count,diffs,new,str(new==correct_barcode)))
        summary[new==correct_barcode][diffs] += count
        
    summary_f.write('%s\tCorrect Barcode\t%d\t%d\t%d\t%d\t%d\t%d\n' %\
     (lane_id,summary[True][0],summary[True][1],summary[True][2],summary[True][3],summary[True][4],summary[True][-1]))
    summary_f.write('%s\tIncorrect Barcode\t%d\t%d\t%d\t%d\t%d\t%d\n' %\
     (lane_id,summary[False][0],summary[False][1],summary[False][2],summary[False][3],summary[False][4],summary[False][-1]))
    all_f.close()
    summary_f.close()
        


if __name__ == "__main__":
    main()