Mercurial > repos > greg > plant_tribes_gene_family_aligner
diff utils.py @ 11:1c5a484fc06f draft default tip
planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/gene_family_aligner commit f7690d10e0515911ee00455806e457bc53f145c7-dirty
author | greg |
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date | Thu, 13 Jun 2024 11:54:31 +0000 |
parents | 79ea0eef1942 |
children |
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--- a/utils.py Tue Sep 04 08:51:38 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,56 +0,0 @@ -import os -import shutil -import subprocess -import sys - -FSTDERR = 'stderr.txt' -FSTDOUT = 'stdout.txt' - - -def check_execution_errors(rc, fstderr, fstdout): - if rc != 0: - fh = open(fstdout, 'rb') - out_msg = fh.read() - fh.close() - fh = open(fstderr, 'rb') - err_msg = fh.read() - fh.close() - msg = '%s\n%s\n' % (str(out_msg), str(err_msg)) - stop_err(msg) - - -def get_response_buffers(): - fstderr = os.path.join(os.getcwd(), FSTDERR) - fherr = open(fstderr, 'wb') - fstdout = os.path.join(os.getcwd(), FSTDOUT) - fhout = open(fstdout, 'wb') - return fstderr, fherr, fstdout, fhout - - -def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False): - source_directory = os.path.abspath(source_dir) - destination_directory = os.path.abspath(destination_dir) - if not os.path.isdir(destination_directory): - os.makedirs(destination_directory) - for dir_entry in os.listdir(source_directory): - source_entry = os.path.join(source_directory, dir_entry) - if copy: - shutil.copy(source_entry, destination_directory) - else: - shutil.move(source_entry, destination_directory) - if remove_source_dir: - os.rmdir(source_directory) - - -def run_command(cmd): - fstderr, fherr, fstdout, fhout = get_response_buffers() - proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True) - rc = proc.wait() - # Check results. - fherr.close() - fhout.close() - check_execution_errors(rc, fstderr, fstdout) - - -def stop_err(msg): - sys.exit(msg)