Convert oligotyping ready fasta files into QIIME ready ones.

qiimize.py

import sys
import Oligotyping.lib.fastalib as u

fasta = u.SequenceSource(sys.argv[1])
output = u.FastaOutput(sys.argv[1] + '-QIIME-READY')


# H12DL4_12 B022DACXX4110133892403 orig_bc=GATCAG new_bc=GATCAG bc_diffs=0
sample_read_counter = {}

while fasta.next():
    if len(fasta.id.split('_')) > 1:
        sample = '_'.join(fasta.id.split('_')[:-1])
        read_id = fasta.id.split('_')[-1].split('|')[0]
    else:
        sample = 'sample'
        read_id = fasta.id


    if not sample_read_counter.has_key(sample):
        sample_read_counter[sample] = 0
    else:
        sample_read_counter[sample] += 1
        current_sample = sample

    output.write_id('%s_%d %s orig_bc=GATCAG new_bc=GATCAG bc_diffs=0' % (sample, sample_read_counter[sample], read_id))
    output.write_seq(fasta.seq, split = False)

fasta.close()
output.close()