Mercurial > repos > greg > plant_tribes_assembly_post_processor
view utils.py @ 10:4d73965d99a2 draft
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/assembly_post_processor commit 71ba0e157346927bf42b788f552b95a71556b28a"
author | greg |
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date | Wed, 09 Jun 2021 20:26:55 +0000 |
parents | b0d9dc3c8535 |
children |
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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)