From a19f61d1395bc557d6b74dc0497014b38aa90d4b Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 25 Jan 2021 12:28:23 -0600
Subject: [PATCH] Convert strandedness from yes/no to t/f
---
workflow/scripts/parse_meta.py | 14 ++------------
1 file changed, 2 insertions(+), 12 deletions(-)
diff --git a/workflow/scripts/parse_meta.py b/workflow/scripts/parse_meta.py
index b5379bb..0b15f07 100644
--- a/workflow/scripts/parse_meta.py
+++ b/workflow/scripts/parse_meta.py
@@ -63,12 +63,7 @@ def main():
# Get strandedness metadata from 'Experiment Settings.csv'
if (args.parameter == "stranded"):
- if (metaFile.Has_Strand_Specific_Information.unique() == "yes"):
- stranded = "stranded"
- elif (metaFile.Has_Strand_Specific_Information.unique() == "no"):
- stranded = "unstranded"
- else:
- stranded = metaFile.Has_Strand_Specific_Information.unique()[0]
+ stranded = metaFile.Stranded.unique()[0]
print(stranded)
# Get spike-in metadata from 'Experiment Settings.csv'
@@ -78,12 +73,7 @@ def main():
# Get species metadata from 'Experiment.csv'
if (args.parameter == "species"):
- if (metaFile.Species.unique() == "Mus musculus"):
- species = "Mus musculus"
- elif (metaFile.Species.unique() == "Homo sapiens"):
- species = "Homo sapiens"
- else:
- species = metaFile.Species.unique()[0]
+ species = metaFile.Species.unique()[0]
print(species)
# Get read length metadata from 'Experiment Settings.csv'
--
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