Mercurial > repos > greg > gene_family_classifier
comparison utils.py @ 142:9fdc9793f9d3 draft
Uploaded
| author | greg |
|---|---|
| date | Fri, 05 May 2017 09:32:30 -0400 |
| parents | |
| children | 5b1873b55da5 |
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| 141:07bf26b7a1ab | 142:9fdc9793f9d3 |
|---|---|
| 1 import os | |
| 2 import shutil | |
| 3 import subprocess | |
| 4 import sys | |
| 5 | |
| 6 FSTDERR = 'stderr.txt' | |
| 7 FSTDOUT = 'stdout.txt' | |
| 8 | |
| 9 | |
| 10 def check_execution_errors(rc, fstderr, fstdout): | |
| 11 if rc != 0: | |
| 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 | |
| 28 | |
| 29 | |
| 30 def move_directory_files(source_dir, destination_dir): | |
| 31 source_directory = os.path.abspath(source_dir) | |
| 32 destination_directory = os.path.abspath(destination_dir) | |
| 33 if not os.path.isdir(destination_directory): | |
| 34 os.makedirs(destination_directory) | |
| 35 for dir_entry in os.listdir(source_directory): | |
| 36 source_entry = os.path.join(source_directory, dir_entry) | |
| 37 shutil.move(source_entry, destination_directory) | |
| 38 | |
| 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 | |
| 50 def stop_err(msg): | |
| 51 sys.exit(msg) | |
| 52 | |
| 53 | |
| 54 def write_html_output(output, title, dir): | |
| 55 with open(output, 'w') as fh: | |
| 56 fh.write('<html><head><h3>%s</h3></head>\n' % title) | |
| 57 fh.write('<body><p/><table cellpadding="2">\n') | |
| 58 fh.write('<tr><th>Size</th><th>Name</th></tr>\n') | |
| 59 for index, fname in enumerate(sorted(os.listdir(dir))): | |
| 60 if index % 2 == 0: | |
| 61 bgcolor = '#D8D8D8' | |
| 62 else: | |
| 63 bgcolor = '#FFFFFF' | |
| 64 try: | |
| 65 size = str(os.path.getsize(os.path.join(dir, fname))) | |
| 66 except: | |
| 67 size = 'unknown' | |
| 68 link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname) | |
| 69 fh.write('<tr bgcolor="%s"><td>%s</td><td>%s</td></tr>\n' % (bgcolor, size, link)) | |
| 70 fh.write('</table></body></html>\n') |