A very quick-and-dirty, untested script to see if it'll be possible to analyze miRNA sequence data in [QIIME](www.qiime.org). Just need this code to perform some initial sequence processing. THIS SCRIPT IS UNTESTED - DO NOT USE FOR ANYTHING IMPORTANT!!!

trim_mirna_adapters.py

#!/usr/bin/env python
# File created on 07 Mar 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 cogent.parse.fastq import MinimalFastqParser
from qiime.util import parse_command_line_parameters, make_option, create_dir

script_info = {}
script_info['brief_description'] = ""
script_info['script_description'] = ""
script_info['script_usage'] = [\
 ("","","%prog -i sample1_input.fastq -o out/ -s sample1 -5 TGGAATTCTCGGGTGCCAAGG")]
script_info['output_description']= ""
script_info['required_options'] = [
 make_option('-i','--input_fp',type="existing_filepath",help='the input filepath'),
 make_option('-s','--sample_id',help='the sample id'),
 make_option('-o','--output_dir',help='the output_directory'),
]
script_info['optional_options'] = [
 make_option('-5','--five_prime_adapter',help='The five prime adaptor sequence'),
 make_option('-m',
             '--five_prime_adapter_max_mismatches',
             default=1,
             type='int',
             help='The five prime adaptor sequence'),
]
script_info['version'] = __version__

def trim_mirna_adapters(input_fastq,
                        sample_id,
                        output_f,
                        five_prime_adapter,
                        five_prime_adapter_max_mismatches):
    """ """
    if five_prime_adapter == None:
        def retain_seq(seq):
            return True, seq
    else:
        five_prime_adapter_len = len(five_prime_adapter)
        def retain_seq(seq):
            count_diffs = 0
            for a,e in zip(seq[:five_prime_adapter_len],five_prime_adapter):
                if a != e:
                    count_diffs += 1
            return count_diffs <= five_prime_adapter_max_mismatches, seq[five_prime_adapter_len:]
            
    i = 0
    for seq_id, seq, qual in input_fastq:
        acceptable_adapter, trimmed_seq = retain_seq(seq)
        if acceptable_adapter:
            output_f.write('>%s_%d %s\n%s\n' % (sample_id,i,seq_id,trimmed_seq))
            i += 1
        else:
            pass

def main():
    option_parser, opts, args =\
       parse_command_line_parameters(**script_info)
    create_dir(opts.output_dir)
    trim_mirna_adapters(MinimalFastqParser(open(opts.input_fp,'U'),strict=False),
                        opts.sample_id,
                        open('%s/%s.fna' % (opts.output_dir,opts.sample_id),'w'),
                        opts.five_prime_adapter,
                        opts.five_prime_adapter_max_mismatches)

if __name__ == "__main__":
    main()