From bdf447e88b75f72ed3fc37acd717ae55daf14ed3 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 9 Jun 2021 10:14:42 +0200
Subject: [PATCH] Fix print, comment solution for kmer counting.
---
source/Collection_Data_Types.rst | 2 +-
source/_static/code/kmer.py | 10 ++++++++--
2 files changed, 9 insertions(+), 3 deletions(-)
diff --git a/source/Collection_Data_Types.rst b/source/Collection_Data_Types.rst
index 5fc4b1a..67769b1 100644
--- a/source/Collection_Data_Types.rst
+++ b/source/Collection_Data_Types.rst
@@ -391,7 +391,7 @@ Compute the 6 mers occurences of the sequence above, and print each 6mer and it'
>>> s = s.replace('\n', '')
>>> kmers = get_kmer_occurences(s, 6)
>>> for kmer in kmers:
- >>> print kmer[0], '..', kmer[1]
+ >>> print(kmer[0], '..', kmer[1])
gcagag .. 2
aacttc .. 1
gcaact .. 1
diff --git a/source/_static/code/kmer.py b/source/_static/code/kmer.py
index ae5ce89..e22fd00 100644
--- a/source/_static/code/kmer.py
+++ b/source/_static/code/kmer.py
@@ -1,12 +1,18 @@
def get_kmer_occurences(seq, kmer_len):
"""
- return a list of tuple
+ return a list of tuple
each tuple contains a kmers present in seq and its occurence
"""
+ # Counter dictionary (keys will be kmers, values will be counts)
kmers = {}
stop = len(seq) - kmer_len
for i in range(stop + 1):
+ # Extract kmer starting at position i
kmer = seq[i: i + kmer_len]
+ # Increment the count for kmer
+ # or create the entry the first time this kmer is seen
+ # using default value 0, plus 1
kmers[kmer] = kmers.get(kmer, 0) + 1
- return kmers.items()
\ No newline at end of file
+ # pairs (kmer, count)
+ return kmers.items()
--
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