Mercurial > repos > greg > gene_family_aligner

comparison utils.py @ 26:959926ea2a66 draft

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Uploaded
author greg
date Fri, 05 May 2017 09:31:41 -0400
parents 6accbd3a1449
children 437a43ec5fb4
comparison
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25:93b1207562d3 26:959926ea2a66
1 import os 1 import os
2 import shutil 2 import shutil
3 import subprocess
3 import sys 4 import sys
4 5
6 FSTDERR = 'stderr.txt'
7 FSTDOUT = 'stdout.txt'
5 8
6 def check_execution_errors(rc, stderr): 9
10 def check_execution_errors(rc, fstderr, fstdout):
7 if rc != 0: 11 if rc != 0:
8 stop_err(stderr.read()) 12 fh = open(fstdout, 'rb')
13 out_msg = fh.read()
14 fh.close()
15 fh = open(fstderr, 'rb')
16 err_msg = fh.read()
17 fh.close()
18 msg = '%s\n%s\n' % (str(out_msg), str(err_msg))
19 stop_err(msg)
20
21
22 def get_response_buffers():
23 fstderr = os.path.join(os.getcwd(), FSTDERR)
24 fherr = open(fstderr, 'wb')
25 fstdout = os.path.join(os.getcwd(), FSTDOUT)
26 fhout = open(fstdout, 'wb')
27 return fherr, fhout
9 28
10 29
11 def move_directory_files(source_dir, destination_dir): 30 def move_directory_files(source_dir, destination_dir):
12 source_directory = os.path.abspath(source_dir) 31 source_directory = os.path.abspath(source_dir)
13 destination_directory = os.path.abspath(destination_dir) 32 destination_directory = os.path.abspath(destination_dir)
16 for dir_entry in os.listdir(source_directory): 35 for dir_entry in os.listdir(source_directory):
17 source_entry = os.path.join(source_directory, dir_entry) 36 source_entry = os.path.join(source_directory, dir_entry)
18 shutil.move(source_entry, destination_directory) 37 shutil.move(source_entry, destination_directory)
19 38
20 39
40 def run_command(cmd):
41 fherr, fhout = get_response_buffers()
42 proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True)
43 rc = proc.wait()
44 # Check results.
45 fherr.close()
46 fhout.close()
47 check_execution_errors(rc, fstderr, fstdout)
48
49
21 def stop_err(msg): 50 def stop_err(msg):
22 sys.stderr.write(msg) 51 sys.exit(msg)
23 sys.exit(1)
24 52
25 53
26 def write_html_output(output, title, dir): 54 def write_html_output(output, title, dir):
27 with open(output, 'w') as fh: 55 with open(output, 'w') as fh:
28 fh.write('<html><head><h3>%s</h3></head>\n' % title) 56 fh.write('<html><head><h3>%s</h3></head>\n' % title)