From 11896ade511c9e9e4878739635f768fc787c611e Mon Sep 17 00:00:00 2001
From: "kathleen.moriarty" <kathleen.moriarty@unibas.ch>
Date: Fri, 3 Dec 2021 23:07:21 +0100
Subject: [PATCH] fix docstring text
---
src/read_sequencing.py | 37 +++++++++++++++++++++----------------
1 file changed, 21 insertions(+), 16 deletions(-)
diff --git a/src/read_sequencing.py b/src/read_sequencing.py
index f970db3..e411e10 100644
--- a/src/read_sequencing.py
+++ b/src/read_sequencing.py
@@ -1,11 +1,18 @@
-""" Read Sequencing
+"""Read Sequencing!
+
+Simulate the sequencing of reads on the template of terminal fragments and simulates reads of these fragments.
Author: Kathleen Moriarty
-Class: Programming for Life Sciences
"""
-def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_seq_cyc):
- """Reads a fasta-formatted file of terminal fragments and simulates reads of these fragments.
+def read_sequencing(
+ frag_file_name,
+ output_file_name,
+ num_reads,
+ read_len,
+ num_seq_cyc,
+) -> None:
+ """Reads a fasta-formatted file of terminal fragments and simulates reads.
Simulate the sequencing of reads on the template of terminal
fragments. Reads are copies of fixed length starting
@@ -13,19 +20,17 @@ def read_sequencing(frag_file_name, output_file_name, num_reads, read_len, num_s
is larger than the fragment length, sequencing would in
principle proceed into the 3' adaptor and then would perhaps
yield random bases. For simplicity, here we assume that random
- nucleotides are introduced in this case.
-
- :param output_file_name: file name where to store the output
- :param num_seq_cyc: integer of number of cycles
- :param read_len: integer of identical read length
- :param num_reads: number of total reads to simulate
- :param frag_file_name: input file of terminal fragments
-
- Output:
- Fasta-formatted file ("../output/reads.csv") of reads of identical length, representing 5’
- ends of the terminal fragments
+ nucleotides are introduced in this case. Saves a fasta-formatted
+ file of reads of identical length, representing 5’
+ ends of the terminal fragments as .txt.
+
+ Args:
+ frag_file_name (string): input file of terminal fragments
+ output_file_name (string): file name where to store the output
+ num_reads: number of total reads to simulate
+ read_len: integer of identical read length
+ num_seq_cyc: integer of number of cycles
"""
-
# Import classes
from random import choices, randrange
import numpy as np
--
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