From 3e933d2d5f764266689fc16eef4c9f6e43ede186 Mon Sep 17 00:00:00 2001
From: "kathleen.moriarty" <kathleen.moriarty@unibas.ch>
Date: Mon, 3 Jan 2022 13:34:49 +0100
Subject: [PATCH] add subpackage with cli
---
src/read_sequencing/__init__.py | 3 ++
src/read_sequencing/cli.py | 53 ++++++++++++++++++++
src/{ => read_sequencing}/read_sequencing.py | 0
3 files changed, 56 insertions(+)
create mode 100644 src/read_sequencing/__init__.py
create mode 100644 src/read_sequencing/cli.py
rename src/{ => read_sequencing}/read_sequencing.py (100%)
diff --git a/src/read_sequencing/__init__.py b/src/read_sequencing/__init__.py
new file mode 100644
index 0000000..b03b3e1
--- /dev/null
+++ b/src/read_sequencing/__init__.py
@@ -0,0 +1,3 @@
+"""Placeholder package."""
+
+__version__ = '0.1.0'
diff --git a/src/read_sequencing/cli.py b/src/read_sequencing/cli.py
new file mode 100644
index 0000000..8451c47
--- /dev/null
+++ b/src/read_sequencing/cli.py
@@ -0,0 +1,53 @@
+import argparse
+from read_sequencing import read_sequencing
+
+
+def parse_args() -> argparse.Namespace:
+ """Parse CLI arguments.
+
+ Returns:
+ Parsed CLI arguments.
+ """
+
+ # initiate parser
+ parser = argparse.ArgumentParser(description='Simulate the Sequencing of Reads')
+
+ # add arguments
+ parser.add_argument('--frag_file_name',
+ type=str,
+ help='input file name')
+
+ parser.add_argument('--output_file_name',
+ type=str,
+ help='output file name')
+
+ parser.add_argument('--num_reads',
+ type=int,
+ help='desired number of reads')
+
+ parser.add_argument('--read_len',
+ type=int,
+ help='length of each read')
+
+ return parser.parse_args()
+
+
+def main() -> None:
+ """Main function.
+
+ Interprets the arguments from the commandline,
+ Runs the functions read_sequencing.
+ """
+
+ args = parse_args()
+ read_sequencing(frag_file_name=args.frag_file_name,
+ output_file_name=args.output_file_name,
+ num_reads=args.num_reads,
+ read_len=args.read_len)
+
+
+if __name__ == '__main__':
+ """Initiates main.
+ Calls main function only if run from commandline, but not if imported.
+ """
+ main()
diff --git a/src/read_sequencing.py b/src/read_sequencing/read_sequencing.py
similarity index 100%
rename from src/read_sequencing.py
rename to src/read_sequencing/read_sequencing.py
--
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