From 1b3ad2f15881f457aac518d104921b814eb356af Mon Sep 17 00:00:00 2001
From: Chris Maffeo <cmaffeo2@illinois.edu>
Date: Tue, 4 Sep 2018 13:26:38 -0500
Subject: [PATCH] Updated dnarbd script to use pathlib and to use file's
basename rather than full path
---
bin/dnarbd | 16 ++++++++--------
1 file changed, 8 insertions(+), 8 deletions(-)
diff --git a/bin/dnarbd b/bin/dnarbd
index cf16d9c..13b4026 100755
--- a/bin/dnarbd
+++ b/bin/dnarbd
@@ -3,6 +3,7 @@
import argparse
import re
+import pathlib
from dnarbd.simulate import multiresolution_simulation as simulate
parser = argparse.ArgumentParser(prog="dnarbd",
@@ -31,24 +32,23 @@ args = parser.parse_args()
if __name__ == '__main__':
- infile = args.input_file
+ infile = pathlib.Path(args.input_file)
try:
- re_result = re.match("(.*)\.([^.]+)",infile)
- prefix = re_result.group(1)
- extension = re_result.group(2).lower()
+ prefix = infile.stem
+ extension = ".".join(infile.suffixes)
except:
raise Exception("Unrecognized input file '{}'".format(infile))
- if extension == 'json':
+ if extension == '.json':
from dnarbd.readers import read_cadnano as read_model
- elif extension == 'ma':
+ elif extension == '.ma':
from dnarbd.readers import read_vhelix as read_model
- elif extension == 'pdb':
+ elif extension == '.pdb':
from dnarbd.readers import read_atomic_pdb as read_model
else:
raise Exception("Unrecognized input file '{}'".format(infile))
- model = read_model( infile )
+ model = read_model( str(infile) )
if args.output_prefix is not None:
prefix = args.output_prefix
--
GitLab