From 559456bbcbbe70a9cec7349aa8ea30f11236b33d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Bertrand=20N=C3=A9ron?= <bneron@pasteur.fr>
Date: Tue, 25 Nov 2014 18:29:03 +0100
Subject: [PATCH] fix fasta_to_one_line function
---
source/Data_Types.rst | 11 ++++++-----
source/_static/code/fasta_to_one_line.py | 6 +++---
2 files changed, 9 insertions(+), 8 deletions(-)
diff --git a/source/Data_Types.rst b/source/Data_Types.rst
index 65de161..100eee4 100644
--- a/source/Data_Types.rst
+++ b/source/Data_Types.rst
@@ -181,8 +181,8 @@ create a representation in fasta format of following sequence :
Exercise
--------
-For the following exercise use the python file :download:`sv40 in fasta <_static/code/sv40.py>` which is a python file with the sequence of sv40 in fasta format
-already embeded, and use python -i sv40.py to work.
+For the following exercise use the python file :download:`sv40 in fasta <_static/code/sv40_file.py>` which is a python file with the sequence of sv40 in fasta format
+already embeded, and use python -i sv40_file.py to work.
how long is the sv40 in bp?
Hint : the fasta header is 61bp long.
@@ -212,14 +212,15 @@ pseudocode:
::
python
- >>> import sv40
+ >>> import sv40_file
>>> import fasta_to_one_line
>>>
- >>> sv40seq = fasta_to_one_line(sv40)
- >>> print len(sv40_sequence)
+ >>> sv40_seq = fasta_to_one_line(sv40_file.sv40_fasta)
+ >>> print len(sv40_seq)
5243
Is that the following enzymes:
+
* BamHI (ggatcc),
* EcorI (gaattc),
* HindIII (aagctt),
diff --git a/source/_static/code/fasta_to_one_line.py b/source/_static/code/fasta_to_one_line.py
index 6ef59c0..86b86b9 100644
--- a/source/_static/code/fasta_to_one_line.py
+++ b/source/_static/code/fasta_to_one_line.py
@@ -1,7 +1,7 @@
-def fasta_2_one_line(seq):
- header_end_at = find('\n')
- seq = seq[:header_end_at + 1]
+def fasta_to_one_line(seq):
+ header_end_at = seq.find('\n')
+ seq = seq[header_end_at + 1:]
seq = seq.replace('\n', '')
return seq
--
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