From f760c6df846c02f5dc2786e10c69d0cdb7d963df Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 6 Jan 2019 20:31:17 -0600
Subject: [PATCH] Change sample names for convert reads.
---
workflow/scripts/convert_reads.py | 2 +-
workflow/tests/test_convert_reads.py | 8 ++++----
2 files changed, 5 insertions(+), 5 deletions(-)
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index 2c39680..d235cfb 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -109,7 +109,7 @@ def main():
# Convert PE or SE to tagAlign
bam_basename = os.path.basename(
- utils.strip_extensions(bam, ['.bam']))
+ utils.strip_extensions(bam, ['.bam', '.dedup']))
tag_filename = bam_basename + '.tagAlign.gz'
convert_mapped(bam, tag_filename)
diff --git a/workflow/tests/test_convert_reads.py b/workflow/tests/test_convert_reads.py
index ff8a003..753b54b 100644
--- a/workflow/tests/test_convert_reads.py
+++ b/workflow/tests/test_convert_reads.py
@@ -9,11 +9,11 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
@pytest.mark.singleend
def test_convert_reads_singleend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.tagAlign.gz'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.filt.nodup.bedse.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.tagAlign.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.bedse.gz'))
@pytest.mark.pairedend
def test_map_qc_pairedend():
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.tagAlign.gz'))
- assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bedpe.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.tagAlign.gz'))
+ assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.bedpe.gz'))
--
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