From 65fba13f7ec143e33d6eb8093b1b94c333f41c82 Mon Sep 17 00:00:00 2001
From: "J.F.J. Laros" <jlaros@obscured.morspoort.fixedpoint.nl>
Date: Thu, 8 Aug 2013 20:36:04 +0200
Subject: [PATCH] Synchronised the sequencer assignment solution with the
slides.
---
sequencer_old.py | 29 +++++++++++++++++------------
1 file changed, 17 insertions(+), 12 deletions(-)
diff --git a/sequencer_old.py b/sequencer_old.py
index 2248e8f..39ceeb3 100644
--- a/sequencer_old.py
+++ b/sequencer_old.py
@@ -32,14 +32,14 @@ class Sequence(object):
class Read(object):
def __init__(self):
- self.read = ""
+ self.read = []
self.qual = []
def __str__(self):
- return self.read
+ return "".join(self.read)
- def add(self, base):
- self.read += base[0]
+ def append(self, base):
+ self.read.append(base[0])
self.qual.append(base[1])
def quality(self):
@@ -48,20 +48,23 @@ class Read(object):
def trim(self, score):
for position in range(len(self.read) - 1, -1, -1):
if self.qual[position] >= score:
- return self.read[:position]
+ self.read = self.read[:position + 1]
+ self.qual = self.qual[:position + 1]
+ break
-def withClass():
+def with_class():
spots = 2
run = Sequence(spots)
reads = [Read() for _ in range(spots)]
for tile in run:
for read_id, base in enumerate(tile):
- reads[read_id].add(base)
+ reads[read_id].append(base)
for i in reads:
print i, i.quality()
- print i.trim(39)
+ i.trim(39)
+ print i, i.quality()
def quality(quals):
return sum(quals) / len(quals)
@@ -69,9 +72,9 @@ def quality(quals):
def trim(read, quals, score):
for position in range(len(read) - 1, 0, -1):
if quals[position] >= score:
- return read[:position]
+ return read[:position + 1], quals[:position + 1]
-def withoutClass():
+def without_class():
spots = 2
run = Sequence(spots)
@@ -84,7 +87,9 @@ def withoutClass():
for read_id, read in enumerate(reads):
print read, quality(quals[read_id])
- print trim(read, quals[read_id], 39)
+ read, quals[read_id] = trim(read, quals[read_id], 39)
+ print read, quality(quals[read_id])
if __name__ == "__main__":
- withoutClass()
+ #without_class()
+ with_class()
--
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