From d9c8e6474921784c1c35ab20893b8490c0d374db Mon Sep 17 00:00:00 2001
From: Samuel Mondal <samuel.mondal@unibas.ch>
Date: Sat, 12 Nov 2022 15:14:52 +0100
Subject: [PATCH] creating functions
---
sequence_extractor/exon_concatenation.py | 34 +++++++++++-------------
sequence_extractor/polyA.py | 6 +++++
2 files changed, 21 insertions(+), 19 deletions(-)
create mode 100644 sequence_extractor/polyA.py
diff --git a/sequence_extractor/exon_concatenation.py b/sequence_extractor/exon_concatenation.py
index 9b2465f..4a2f960 100644
--- a/sequence_extractor/exon_concatenation.py
+++ b/sequence_extractor/exon_concatenation.py
@@ -1,19 +1,15 @@
-fa = open("fasta.fa",'r')
-lines = fa.readlines()
-for x in range(int(len(lines)/2)):
- if x == 0:
- annotation = lines[0]
- read = lines[1]
- if x >= 1:
- if lines[2*x] == lines[2*(x-1)]:
- read+= lines[(2*x)+1]
- else:
- annotation = lines[2*x]
- read = lines[(2*x)+1]
-
-# Function for random addition of polyA to sequences
-
-import numpy as np
-
-listA = ['A','U','G','C']
-''.join(np.random.choice(listA,250,p=[0.9,0.040,0.020,0.020]))
+def exon_concatenation:
+ fa = open("fasta.fa",'r')
+ lines = fa.readlines()
+ for x in range(int(len(lines)/2)):
+ if x == 0:
+ annotation = lines[0]
+ read = lines[1]
+ if x >= 1:
+ if lines[2*x] == lines[2*(x-1)]:
+ read+= lines[(2*x)+1]
+ else:
+ return annotation
+ return read
+ annotation = lines[2*x]
+ read = lines[(2*x)+1]
diff --git a/sequence_extractor/polyA.py b/sequence_extractor/polyA.py
new file mode 100644
index 0000000..2c88e79
--- /dev/null
+++ b/sequence_extractor/polyA.py
@@ -0,0 +1,6 @@
+import numpy as np
+
+def PolyA_generator(exon):
+ listA = ['A','T','G','C']
+ polyA = ''.join(np.random.choice(listA,250,p=[0.9,0.040,0.020,0.020]))
+ return (exon+polyA)
--
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