From 17fd164c3356a87adb889d2338b298041dcfb853 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 22 Oct 2017 20:35:20 -0500
Subject: [PATCH] Fix passing of bedpe reads.
---
workflow/main.nf | 2 +-
workflow/scripts/convert_reads.py | 9 ++++++---
workflow/tests/test_convert_reads.py | 1 +
3 files changed, 8 insertions(+), 4 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index a71f30d..70ea405 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -203,7 +203,7 @@ process convertReads {
output:
- set sampleId, file('*.tagAlign.gz'), file('*.bedpe.gz'), biosample, factor, treatment, replicate, controlId into tagReads
+ set sampleId, file('*.tagAlign.gz'), file('*.bed{pe,se}.gz'), biosample, factor, treatment, replicate, controlId into tagReads
script:
diff --git a/workflow/scripts/convert_reads.py b/workflow/scripts/convert_reads.py
index 8019f15..8c090ae 100644
--- a/workflow/scripts/convert_reads.py
+++ b/workflow/scripts/convert_reads.py
@@ -64,10 +64,9 @@ def check_tools():
raise Exception('Missing samtools')
-def convert_mapped(bam, bam_basename):
+def convert_mapped(bam, tag_filename):
'''Use bedtools to convert to tagAlign.'''
- tag_filename = bam_basename + '.tagAlign.gz'
out, err = utils.run_pipe([
"bamToBed -i %s" % (bam),
r"""awk 'BEGIN{OFS="\t"}{$4="N";$5="1000";print $0}'""",
@@ -110,10 +109,14 @@ def main():
bam_basename = os.path.basename(
utils.strip_extensions(bam, ['.bam']))
- convert_mapped(bam, bam_basename)
+ tag_filename = bam_basename + 'tagAlign.gz'
+ convert_mapped(bam, tag_filename)
if paired: # paired-end data
convert_mapped_pe(bam, bam_basename)
+ else:
+ bedse_filename = bam_basename + ".bedse.gz"
+ shutil(tag_filename, bedse_filename)
if __name__ == '__main__':
diff --git a/workflow/tests/test_convert_reads.py b/workflow/tests/test_convert_reads.py
index 8d25fbc..6be1f96 100644
--- a/workflow/tests/test_convert_reads.py
+++ b/workflow/tests/test_convert_reads.py
@@ -9,6 +9,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
def test_convert_reads_singleend():
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'))
def test_map_qc_pairedend():
--
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