From d6a5bea01c74b36d71b0f16c3109b27cf95d2088 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 10 Oct 2017 13:04:13 -0500
Subject: [PATCH] Update triming to have generalized paths.
---
workflow/tests/test_trim_reads.py | 16 ++++++++++------
1 file changed, 10 insertions(+), 6 deletions(-)
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index e9680f6..5ab6b67 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -3,14 +3,18 @@
import pytest
import os
+test_data_path = os.path.dirname(os.path.abspath(__file__)) + \
+ '/../../test_data/'
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+ '/../output/trimReads/'
+
def test_trim_reads_singleend():
- raw_fastq = os.path.dirname(os.path.abspath(__file__)) + \
- '/../../test_data/ENCFF833BLU.fastq.gz'
- trimmed_fastq = os.path.dirname(os.path.abspath(__file__)) + \
- '/../output/trimReads/ENCFF833BLU_trimmed.fq.gz'
- trimmed_fastq_report = os.path.dirname(os.path.abspath(__file__)) + \
- '/../output/trimReads/ENCFF833BLU.fastq.gz_trimming_report.txt'
+ raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
+ trimmed_fastq = test_output_path + 'ENCFF833BLU_trimmed.fq.gz'
+ trimmed_fastq_report = test_output_path + \
+ 'ENCFF833BLU.fastq.gz_trimming_report.txt'
assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
assert os.path.getsize(trimmed_fastq) == 2512853101
assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
--
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