From 2ae7fd8a9b0cfd8fb7ce9a3cfb47f2ef0db5e449 Mon Sep 17 00:00:00 2001
From: "hugo.madgeleon" <hugo.madgeleon@stud.unibas.ch>
Date: Sun, 13 Nov 2022 12:35:29 +0100
Subject: [PATCH] Add check for positive integers in argparse
---
frag_package/fragmentation_v2.py | 13 ++++++++++---
1 file changed, 10 insertions(+), 3 deletions(-)
diff --git a/frag_package/fragmentation_v2.py b/frag_package/fragmentation_v2.py
index eec7aff..a27a493 100644
--- a/frag_package/fragmentation_v2.py
+++ b/frag_package/fragmentation_v2.py
@@ -63,14 +63,21 @@ def extant_file(x):
raise argparse.ArgumentTypeError("{0} does not exist".format(x))
return x
+# found on https://stackoverflow.com/questions/14117415/in-python-using-argparse-allow-only-positive-integers
+def check_positive(value):
+ ivalue = int(value)
+ if ivalue <= 0:
+ raise argparse.ArgumentTypeError("%s is an invalid positive int value" % value)
+ return ivalue
+
# Parse command-line arguments
def parse_arguments():
parser = argparse.ArgumentParser(description="Takes as input FASTA file of cDNA sequences, a CSV with sequence counts, and mean and std. dev. of fragment lengths. Outputs most terminal fragment (within desired length range) for each sequence.")
-
+
parser.add_argument('--fasta', required=True, type=extant_file, help="FASTA file with cDNA sequences")
parser.add_argument('--counts', required=True, type=extant_file, help="CSV file with sequence counts")
- parser.add_argument('--mean', required = False, default = 10, type = int, help="Mean fragment length (default: 10)")
- parser.add_argument('--std', required = False, default = 1, type = int, help="Standard deviation fragment length (defafult: 1)")
+ parser.add_argument('--mean', required = False, default = 10, type = check_positive, help="Mean fragment length (default: 10)")
+ parser.add_argument('--std', required = False, default = 1, type = check_positive, help="Standard deviation fragment length (defafult: 1)")
args = parser.parse_args()
return args.fasta, args.counts, args.mean, args.std
--
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