Removed old assignment.

make_fastq/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()

make_fastq/make_fastq.py

-#!/usr/bin/env python
-
-from sequencer import Sequencer
-
-if __name__ == "__main__":
-    for tile in Sequencer(20):
-        print tile

make_fastq/sequencer.py

-#!/usr/bin/env python
-
-import random
-
-class Sequencer(object):
-    """
-    Simulate a sequencing run.
-
-    For every iteration, return a tile of data points as a list of tuples. The
-    first element of the tuple contains the nucleotide, the second element
-    contains the quality score.
-    """
-    bases = ['A', 'C', 'G', 'T']
-
-    def __init__(self, spots, readlength=100):
-        self.cycle = 0
-        self.readlength = readlength
-        self.spots = spots
-
-    def __iter__(self):
-        return self
-
-    def __len__(self):
-        return self.readlength
-
-    def next(self):
-        self.cycle += 1
-        if self.cycle > self.readlength:
-            raise StopIteration
-
-        tile = []
-        for _ in range(self.spots):
-            nucleotide = self.bases[random.randrange(4)]
-            quality = 40 - (self.cycle * random.randrange(40) /
-                self.readlength)
-            tile.append((nucleotide, quality))
-
-        return tile