example.py

#!/usr/bin/env python

from sequencer import Sequencer

def quality(quals):
    return sum(quals) / len(quals)

def trim(read, quals, score):
    for position in range(len(read) - 1, -1, -1):
        if quals[position] >= score:
            return read[:position + 1], quals[:position + 1]

def make_fastq():
    spots = 2
    run = Sequencer(spots)

    reads = ["" for _ in range(spots)]
    quals = [[] for _ in range(spots)]
    for tile in run:
        for read_id, base in enumerate(tile):
            reads[read_id] += base[0]
            quals[read_id].append(base[1])

    for read_id, read in enumerate(reads):
        print read, quality(quals[read_id])
        read, quals[read_id] = trim(read, quals[read_id], 39)
        print read, quality(quals[read_id])

if __name__ == "__main__":
    make_fastq()