Mercurial > repos > greg > plant_tribes_gene_family_phylogeny_builder
comparison utils.py @ 0:7000422fbaff draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 08 Jun 2017 12:51:58 -0400 |
| parents | |
| children | a7867769a706 |
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| -1:000000000000 | 0:7000422fbaff |
|---|---|
| 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 fstderr, fherr, fstdout, fhout | |
| 28 | |
| 29 | |
| 30 def move_directory_files(source_dir, destination_dir, copy=False): | |
| 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 if copy: | |
| 38 shutil.copy(source_entry, destination_directory) | |
| 39 else: | |
| 40 shutil.move(source_entry, destination_directory) | |
| 41 | |
| 42 | |
| 43 def run_command(cmd): | |
| 44 fstderr, fherr, fstdout, fhout = get_response_buffers() | |
| 45 proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True) | |
| 46 rc = proc.wait() | |
| 47 # Check results. | |
| 48 fherr.close() | |
| 49 fhout.close() | |
| 50 check_execution_errors(rc, fstderr, fstdout) | |
| 51 | |
| 52 | |
| 53 def stop_err(msg): | |
| 54 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') |