Mercurial > repos > greg > plant_tribes_gene_family_aligner

comparison utils.py @ 6:3384b6a842b0 draft

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author greg
date Mon, 30 Oct 2017 09:52:00 -0400
parents 7ba9469800b9
children
comparison
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5:a73c2e65098e 6:3384b6a842b0
25 fstdout = os.path.join(os.getcwd(), FSTDOUT) 25 fstdout = os.path.join(os.getcwd(), FSTDOUT)
26 fhout = open(fstdout, 'wb') 26 fhout = open(fstdout, 'wb')
27 return fstderr, fherr, fstdout, fhout 27 return fstderr, fherr, fstdout, fhout
28 28
29 29
30 def move_directory_files(source_dir, destination_dir, copy=False): 30 def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
31 source_directory = os.path.abspath(source_dir) 31 source_directory = os.path.abspath(source_dir)
32 destination_directory = os.path.abspath(destination_dir) 32 destination_directory = os.path.abspath(destination_dir)
33 if not os.path.isdir(destination_directory): 33 if not os.path.isdir(destination_directory):
34 os.makedirs(destination_directory) 34 os.makedirs(destination_directory)
35 for dir_entry in os.listdir(source_directory): 35 for dir_entry in os.listdir(source_directory):
36 source_entry = os.path.join(source_directory, dir_entry) 36 source_entry = os.path.join(source_directory, dir_entry)
37 if copy: 37 if copy:
38 shutil.copy(source_entry, destination_directory) 38 shutil.copy(source_entry, destination_directory)
39 else: 39 else:
40 shutil.move(source_entry, destination_directory) 40 shutil.move(source_entry, destination_directory)
41 if remove_source_dir:
42 os.rmdir(source_directory)
41 43
42 44
43 def run_command(cmd): 45 def run_command(cmd):
44 fstderr, fherr, fstdout, fhout = get_response_buffers() 46 fstderr, fherr, fstdout, fhout = get_response_buffers()
45 proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True) 47 proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True)
50 check_execution_errors(rc, fstderr, fstdout) 52 check_execution_errors(rc, fstderr, fstdout)
51 53
52 54
53 def stop_err(msg): 55 def stop_err(msg):
54 sys.exit(msg) 56 sys.exit(msg)
55
56
57 def write_html_output(output, title, dir):
58 with open(output, 'w') as fh:
59 dir_items = sorted(os.listdir(dir))
60 # Directories can only contain either files or directories,
61 # but not both.
62 if len(dir_items) > 0:
63 item_path = os.path.join(dir, dir_items[0])
64 if os.path.isdir(item_path):
65 header = 'Directories'
66 else:
67 header = 'Datasets'
68 else:
69 header = ''
70 fh.write('<html><head><h3>%s: %d items</h3></head>\n' % (title, len(dir_items)))
71 fh.write('<body><p/><table cellpadding="2">\n')
72 fh.write('<tr><b>%s</th></b>\n' % header)
73 for index, fname in enumerate(dir_items):
74 if index % 2 == 0:
75 bgcolor = '#D8D8D8'
76 else:
77 bgcolor = '#FFFFFF'
78 link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname)
79 fh.write('<tr bgcolor="%s"><td>%s</td></tr>\n' % (bgcolor, link))
80 fh.write('</table></body></html>\n')