From 4b810197653c367c3376a0b8c067a9b9aba7c3cc Mon Sep 17 00:00:00 2001
From: LauraU123 <laura.urbanska@stud.unibas.ch>
Date: Wed, 9 Nov 2022 10:25:00 +0100
Subject: [PATCH] added argparse part
---
scripts/argparse_example.py | 31 +++++++++++++++++++++++++++++++
1 file changed, 31 insertions(+)
create mode 100644 scripts/argparse_example.py
diff --git a/scripts/argparse_example.py b/scripts/argparse_example.py
new file mode 100644
index 0000000..7068aaa
--- /dev/null
+++ b/scripts/argparse_example.py
@@ -0,0 +1,31 @@
+import argparse
+
+if __name__ == '__main__':
+ parser = argparse.ArgumentParser(
+ description="transcript sampler",
+ formatter_class=argparse.ArgumentDefaultsHelpFormatter
+ )
+ parser.add_argument("--annotation", required=True, help="gtf file with genome annotation")
+ parser.add_argument("--expression_level", required=True, help="csv file with expression level")
+ parser.add_argument("--output_csv", required=True, help="output csv file")
+ parser.add_argument("--output_gtf", required=True, help="output gtf file")
+ parser.add_argument("--transcript_number", required=True, help="total number of transcripts to sample")
+ args = parser.parse_args()
+
+
+
+# script name being whatever we call our workflow class/function that takes the inputs
+ script_name(args.annotation, args.expression_level, args.output_csv, args.output_gtf, args.transcript_number)
+
+
+"""note:
+so to run our entire workflow, it will suffice to type the following into the command line:
+ python filename.py \
+ --annotation filename1.gtf \
+ --expression_level filename2.gtf \
+ --output_csv output1.csv \
+ --output_gtf output2.gtf \
+ --transcript_number 100 (some number)
+
+
+"""
\ No newline at end of file
--
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