From 1efe9b84296d8d1659f7169187dfb5436a9b838c Mon Sep 17 00:00:00 2001
From: garion0000 <michele.garioni@unibas.ch>
Date: Wed, 8 Dec 2021 11:25:05 +0100
Subject: [PATCH] fix: add cli
---
src/{sampleinput.py => sample_from_input.py} | 27 ++++++++++++++++++++
1 file changed, 27 insertions(+)
rename src/{sampleinput.py => sample_from_input.py} (69%)
diff --git a/src/sampleinput.py b/src/sample_from_input.py
similarity index 69%
rename from src/sampleinput.py
rename to src/sample_from_input.py
index a6cc7e7..817d96b 100644
--- a/src/sampleinput.py
+++ b/src/sample_from_input.py
@@ -71,3 +71,30 @@ def sample_from_input(
myfile.write(line + '\n')
myfile.close()
LOG.info('output written.')
+
+
+def main():
+ """CLI interface for the transcripts sampler.
+
+ Accepts arguments from the command line and
+ runs the transcript sampler.
+ """
+ import argparse
+ parser = argparse.ArgumentParser(description='Read functions argument')
+ parser.add_argument('input', action='store',
+ type=Path, help='path of the input file')
+ parser.add_argument('-o', action='store',
+ type=Path, default=Path.cwd() / 'sampled_cell.csv',
+ help='path of the output file')
+ parser.add_argument('-n', action='store',
+ type=int, default=10000,
+ help='number of total reads to be simulated')
+ parser.add_argument('-sep', action='store',
+ type=str, default=',',
+ help='separator of the input file')
+ args = parser.parse_args()
+ sample_from_input(args.input, args.o, args.n, args.sep)
+
+
+if __name__ == '__main__':
+ main()
--
GitLab