From e8b92b99929afd08adfdd5f0d1c2fe857d6e0562 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 3 Aug 2020 14:23:28 -0500
Subject: [PATCH] Extract read length from submitter metadata
---
.gitlab-ci.yml | 3 ++-
workflow/rna-seq.nf | 8 +++++++-
workflow/scripts/parseMeta.py | 5 +++++
workflow/tests/test_parseMetadata.py | 2 +-
4 files changed, 15 insertions(+), 3 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index b36504f..29f4925 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -38,7 +38,8 @@ parseMetadata:
- stranded=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p stranded)
- spike=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p spike)
- species=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.csv" -p species)
- - echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${exp},${study},${rep}" > design.csv
+ - readLength=$(singularity run 'docker://bicf/python3:2.0.1_indev' python3 ./workflow/scripts/parseMeta.py -r Replicate_RID -m "./test_data/meta/metaTest.stageNew.csv" -p readLength)
+ - echo -e "${endsMeta},${endsManual},${stranded},${spike},${species},${readLength},${exp},${study},${rep}" > design.csv
- pytest -m parseMetadata
inferMetadata:
diff --git a/workflow/rna-seq.nf b/workflow/rna-seq.nf
index 2e1e2b2..1443869 100644
--- a/workflow/rna-seq.nf
+++ b/workflow/rna-seq.nf
@@ -237,8 +237,12 @@ process parseMetadata {
species=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p species)
echo -e "LOG: species metadata parsed: \${species}" >> ${repRID}.parseMetadata.log
+ # get read length metadata
+ readLength=\$(python3 ${script_parseMeta} -r ${repRID} -m "${experiment}" -p readLength)
+ echo -e "LOG: read length metadata parsed: \${readLength}" >> ${repRID}.parseMetadata.log
+
# gave design file
- echo -e "\${endsMeta},\${endsManual},\${stranded},\${spike},\${species},\${exp},\${study}" > design.csv
+ echo -e "\${endsMeta},\${endsManual},\${stranded},\${spike},\${species},\${readLength},\${exp},\${study}" > design.csv
"""
}
@@ -248,6 +252,7 @@ endsManual = Channel.create()
strandedMeta = Channel.create()
spikeMeta = Channel.create()
speciesMeta = Channel.create()
+readLengthMeta = Channel.create()
expRID = Channel.create()
studyRID = Channel.create()
metadata.splitCsv(sep: ",", header: false).separate(
@@ -256,6 +261,7 @@ metadata.splitCsv(sep: ",", header: false).separate(
strandedMeta,
spikeMeta,
speciesMeta,
+ readLengthMeta,
expRID,
studyRID
)
diff --git a/workflow/scripts/parseMeta.py b/workflow/scripts/parseMeta.py
index fd73cf3..453e418 100644
--- a/workflow/scripts/parseMeta.py
+++ b/workflow/scripts/parseMeta.py
@@ -102,5 +102,10 @@ def main():
exit(1)
print(species)
+ # Get read length metadata from 'Experiment Settings.csv'
+ if (args.parameter == "readLength"):
+ readLength = metaFile.Read_Length.unique()
+ print(readLength)
+
if __name__ == '__main__':
main()
diff --git a/workflow/tests/test_parseMetadata.py b/workflow/tests/test_parseMetadata.py
index 31a9674..59677bb 100644
--- a/workflow/tests/test_parseMetadata.py
+++ b/workflow/tests/test_parseMetadata.py
@@ -17,7 +17,7 @@ def readLine(fileName):
data = False
file = open(fileName, "r")
line = file.readline()
- if line.strip() == "uk,se,unstranded,no,Homo sapiens,Experiment_RID,Study_RID,Replicate_RID":
+ if line.strip() == "uk,se,unstranded,no,Homo sapiens,75,Experiment_RID,Study_RID,Replicate_RID":
data = True
return data
--
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