From 6adfc082a0fbcc35f50ef2b7303e32707d24d24c Mon Sep 17 00:00:00 2001
From: Samuel Mondal <samuel.mondal@unibas.ch>
Date: Sat, 26 Nov 2022 23:53:16 +0100
Subject: [PATCH 1/2] Changing output from a list to a list of tuples
---
sequence_extractor/exon_concatenation.py | 6 ++----
1 file changed, 2 insertions(+), 4 deletions(-)
diff --git a/sequence_extractor/exon_concatenation.py b/sequence_extractor/exon_concatenation.py
index 666c303..d95ef0a 100644
--- a/sequence_extractor/exon_concatenation.py
+++ b/sequence_extractor/exon_concatenation.py
@@ -20,10 +20,8 @@ def exon_concatenation(
if annotation[-1] == line1[0:16]:
read += line2[:-1]
elif annotation[-1] != line1[0:16]:
- fasta_format_list.append(annotation[-1])
- fasta_format_list.append(read)
+ fasta_format_list.append((annotation[-1],read))
annotation.append(line1[0:16])
read = line2[:-1]
- fasta_format_list.append(annotation[-1])
- fasta_format_list.append(read)
+ fasta_format_list.append((annotation[-1],read))
return fasta_format_list
--
GitLab
From 834f7fbc93be78818b54eeebb2fa37fe54799b68 Mon Sep 17 00:00:00 2001
From: Samuel Mondal <samuel.mondal@unibas.ch>
Date: Sat, 26 Nov 2022 23:55:19 +0100
Subject: [PATCH 2/2] Changing to a list of tuples (much more simplified)
---
sequence_extractor/polyA.py | 10 ++--------
1 file changed, 2 insertions(+), 8 deletions(-)
diff --git a/sequence_extractor/polyA.py b/sequence_extractor/polyA.py
index 137ad6e..8c1715a 100644
--- a/sequence_extractor/polyA.py
+++ b/sequence_extractor/polyA.py
@@ -26,11 +26,5 @@ def polyA_addition_to_fasta_list(
Returns:
A list like the initial list, this time with polyA tail added onto it.
"""
- list_annotation = fasta_list[0::2]
- list_exon = fasta_list[1::2]
- mature_rna_list = [polyA_generator(i) for i in list_exon]
- final_list = []
- for annotation, exon in zip(list_annotation,mature_rna_list):
- final_list.append(annotation)
- final_list.append(exon)
- return final_list
+ mature_rna_list = [(i[0],polyA_generator(i[1])) for i in fasta_list]
+ return mature_rna_list
--
GitLab