From 7179e4ed65730351a29b5febaaf65bf4b705dca1 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Thu, 30 Jul 2020 13:27:02 -0500
Subject: [PATCH] Test for pytest for parseMetadata: supposed to pass #54
---
.gitlab-ci.yml | 3 ++-
workflow/tests/test_parseMetadata.py | 2 +-
2 files changed, 3 insertions(+), 2 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ad7330b..3491d36 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -121,7 +121,8 @@ dataQC:
stage: unit
script:
- echo -e "geneID\tchrom\ttx_start\ttx_end\tTIN" > Q-Y5F6_1M.se.sorted.deduped.tin.xls
-
+ - for i in {"chr8","chr4","chrY"}; do
+ echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
- pytest -m dataQC
diff --git a/workflow/tests/test_parseMetadata.py b/workflow/tests/test_parseMetadata.py
index e15f7c8..bede55f 100644
--- a/workflow/tests/test_parseMetadata.py
+++ b/workflow/tests/test_parseMetadata.py
@@ -16,7 +16,7 @@ def test_parseMetadata():
def readLine(fileName):
data = False
file = open(fileName, "r")
- if file.readline() == "uk,se,unstranded,no,Homo sapiens,Experiment_RID,Study_RID,Replicate_RID":
+ if file.readline()[] == "uk,se,unstranded,no,Homo sapiens,Experiment_RID,Study_RID,Replicate_RID":
data = True
return data
--
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