From d3ccefa86675430a3f6f9755bdec57cf4945707a Mon Sep 17 00:00:00 2001
From: "kathleen.moriarty" <kathleen.moriarty@unibas.ch>
Date: Wed, 8 Dec 2021 18:15:34 +0100
Subject: [PATCH] added: comments and new lines
---
src/read_sequencing.py | 5 +++--
tests/test_read_sequence.py | 6 +++---
2 files changed, 6 insertions(+), 5 deletions(-)
diff --git a/src/read_sequencing.py b/src/read_sequencing.py
index e229af2..2382f51 100644
--- a/src/read_sequencing.py
+++ b/src/read_sequencing.py
@@ -1,4 +1,4 @@
-"""Read Sequencing!
+"""Read Sequencing.
Simulate the sequencing of reads on the template of terminal fragments and simulates reads of these fragments.
Author: Kathleen Moriarty
@@ -33,14 +33,15 @@ def read_sequencing(
num_reads: number of total reads to simulate
read_len: integer of identical read length
"""
-
# Read data from terminal fragment file
# Store fragment descriptions in a list
frag_desc = [] # type: List[str]
with open(frag_file_name, 'r') as f:
frag_line = f.readline()
+ # Store all fragments as a list to parse later
frag_list = [] # type: List[str]
+ # Store combined fragment lines
frag_str = ""
while frag_line != "":
# To stop when the end of file is reached
diff --git a/tests/test_read_sequence.py b/tests/test_read_sequence.py
index bae061e..3b1021b 100644
--- a/tests/test_read_sequence.py
+++ b/tests/test_read_sequence.py
@@ -1,4 +1,4 @@
-"""Test Read Sequencing Functionality."""
+"""Test Functionality of Read Sequencing"""
# imports from built-in modules
from pathlib import Path
@@ -13,10 +13,10 @@ from src.read_sequencing import read_sequencing
def test_read_sequencing(tmpdir):
"""Tests the correct number of reads were generated."""
read_sequencing(
- frag_file_name=Path('./tests/resources/test_terminal_fragments.txt'),
+ frag_file_name=Path.cwd() / 'tests/resources/test_terminal_fragments.txt',
num_reads=80,
read_len=10,
output_file_name=tmpdir / 'reads.txt'
)
df_out = pd.read_table(tmpdir / 'reads.txt', header=None)
- assert df_out.shape[0] == 80 * 3
+ assert df_out.shape[0] == 80 * 2
--
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