From 6c08c421340d8c789272b4f55547782677dd6230 Mon Sep 17 00:00:00 2001 From: Gertjan Bisschop Date: Sun, 5 Nov 2023 15:23:13 +0000 Subject: [PATCH 1/2] fix import error --- gimbleprep.py | 2 +- gimbleprep/preprocess.py | 10 ++++++---- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/gimbleprep.py b/gimbleprep.py index c6b1e1a..4bcfb84 100755 --- a/gimbleprep.py +++ b/gimbleprep.py @@ -2,7 +2,7 @@ # -*- coding: utf-8 -*- import os -from cli.interface import main +from gimbleprep.interface import main if __name__ == '__main__': main(os.path.dirname(os.path.realpath(__file__))) diff --git a/gimbleprep/preprocess.py b/gimbleprep/preprocess.py index 00e4e6d..8615105 100644 --- a/gimbleprep/preprocess.py +++ b/gimbleprep/preprocess.py @@ -15,7 +15,6 @@ -h, --help Show this """ -import gimbleprep.runargs import numpy as np import tempfile import pathlib @@ -26,6 +25,9 @@ from tqdm import tqdm import pysam import pandas as pd + +import gimbleprep.runargs as runargs + from timeit import default_timer as timer from docopt import docopt @@ -68,7 +70,7 @@ def fix_permissions(path): os.chmod(_f, 0o664) #os.chmod(root, 0o775) -class PreprocessParameterObj(lib.runargs.RunArgs): +class PreprocessParameterObj(runargs.RunArgs): '''Sanitises command line arguments and stores parameters''' def __init__(self, params, args): super().__init__(params) @@ -271,7 +273,7 @@ def main(params): parameterObj = PreprocessParameterObj(params, args) print("[+] Running 'gimble-preprocess'...") preprocess(parameterObj) - print("[*] Total runtime was %s" % (lib.runargs.format_time(timer() - start_time))) + print("[*] Total runtime was %s" % (runargs.format_time(timer() - start_time))) except KeyboardInterrupt: - print("\n[X] Interrupted by user after %s !\n" % (lib.runargs.format_time(timer() - start_time))) + print("\n[X] Interrupted by user after %s !\n" % (runargs.format_time(timer() - start_time))) exit(-1) From 8150e066eb7f6effab5f15059fe206ac0e56ec30 Mon Sep 17 00:00:00 2001 From: Gertjan Bisschop Date: Sun, 5 Nov 2023 15:25:02 +0000 Subject: [PATCH 2/2] versionbump --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 58540b1..6218626 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ setup( name='gimbleprep', - version='0.0.2b4', + version='0.0.2b5', description='Preprocess fasta, bam and vcf files ready to be used by gimble', url='http://github.com/LohseLab/gimbleprep', author='Lohse Lab',