From f0fbf42b59da5a84d55c97fa61b67d4806266f60 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 8 Oct 2017 22:17:26 -0500
Subject: [PATCH] Add in test for verifying single end trim reads.
---
workflow/tests/test_trim_reads.py | 13 +++++++++----
1 file changed, 9 insertions(+), 4 deletions(-)
diff --git a/workflow/tests/test_trim_reads.py b/workflow/tests/test_trim_reads.py
index cd15430..c7821f0 100644
--- a/workflow/tests/test_trim_reads.py
+++ b/workflow/tests/test_trim_reads.py
@@ -6,10 +6,15 @@ import gzip
def test_trim_reads_singleend():
- # assert os.path.getsize('sample1_R1.fastq.gz') != os.path.getsize('sample1_R1.trim.fastq.gz')
- # check the size of the lines using
- # a = sum(1 for _ in gzip.open('input_2.small_R1.fastq.gz'))
- pass
+ 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')
+ 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]
def test_trim_reads_pairedend():
--
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