Added an example solution for the sequencer 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()