Mercurial > repos > greg > gene_family_classifier
diff gene_family_classifier.py @ 131:656614635ebf draft
Uploaded
| author | greg |
|---|---|
| date | Thu, 06 Apr 2017 14:21:39 -0400 |
| parents | 7789adec8707 |
| children | b2ae23e484e8 |
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--- a/gene_family_classifier.py Wed Mar 22 08:45:31 2017 -0400 +++ b/gene_family_classifier.py Thu Apr 06 14:21:39 2017 -0400 @@ -3,8 +3,9 @@ import os import shutil import subprocess -import sys -import tempfile + +import utils + BUFF_SIZE = 1048576 OUTPUT_DIR = 'geneFamilyClassification_dir' @@ -34,79 +35,6 @@ args = parser.parse_args() -def get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout, include_stdout=False): - tmp_stderr.close() - """ - Return a stderr string of reasonable size. - """ - # Get stderr, allowing for case where it's very large. - tmp_stderr = open(tmp_err, 'rb') - stderr_str = '' - buffsize = BUFF_SIZE - try: - while True: - stderr_str += tmp_stderr.read(buffsize) - if not stderr_str or len(stderr_str) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if include_stdout: - tmp_stdout = open(tmp_out, 'rb') - stdout_str = '' - buffsize = BUFF_SIZE - try: - while True: - stdout_str += tmp_stdout.read(buffsize) - if not stdout_str or len(stdout_str) % buffsize != 0: - break - except OverflowError: - pass - tmp_stdout.close() - if include_stdout: - return 'STDOUT\n%s\n\nSTDERR\n%s\n' % (stdout_str, stderr_str) - return stderr_str - - -def move_directory_files(source_dir, destination_dir): - 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) - shutil.move(source_entry, destination_directory) - - -def stop_err(msg): - sys.stderr.write(msg) - sys.exit(1) - - -def write_html_output(output, title, dir): - with open(output, 'w') as fh: - fh.write('<html><head><h3>%s</h3></head>\n' % title) - fh.write('<body><p/><table cellpadding="2">\n') - fh.write('<tr><th>Size</th><th>Name</th></tr>\n') - for index, fname in enumerate(sorted(os.listdir(dir))): - if index % 2 == 0: - bgcolor = '#D8D8D8' - else: - bgcolor = '#FFFFFF' - try: - size = str(os.path.getsize(os.path.join(dir, fname))) - except: - size = 'unknown' - link = '<a href="%s" type="text/plain">%s</a>\n' % (fname, fname) - fh.write('<tr bgcolor="%s"><td>%s</td><td>%s</td></tr>\n' % (bgcolor, size, link)) - fh.write('</table></body></html>\n') - - -# Define command response buffers. -tmp_out = tempfile.NamedTemporaryFile().name -tmp_stdout = open(tmp_out, 'wb') -tmp_err = tempfile.NamedTemporaryFile().name -tmp_stderr = open(tmp_err, 'wb') # Build the command line. cmd = 'GeneFamilyClassifier' cmd += ' --proteins %s' % args.input @@ -134,12 +62,9 @@ create_corresponding_coding_sequences = True cmd += ' --coding_sequences %s' % args.coding_sequences # Run the command. -proc = subprocess.Popen(args=cmd, stderr=tmp_stderr, stdout=tmp_stdout, shell=True) +proc = subprocess.Popen(args=cmd, stderr=subprocess.PIPE, stdout=subprocess.PIPE, shell=True) rc = proc.wait() -# Handle execution errors. -if rc != 0: - error_message = get_stderr_exception(tmp_err, tmp_stderr, tmp_out, tmp_stdout) - stop_err( error_message ) +utils.check_execution_errors(rc, proc.stderr) # Handle hmmscan.log output. if args.classifier in ['hmmscan', 'both']: src_hmmscan_log = os.path.join(OUTPUT_DIR, 'hmmscan.log') @@ -159,12 +84,12 @@ orthogroups_fasta_dest_dir = args.output_ptortho_dir title = 'Orthogroups files' orthogroups_fasta_src_dir = os.path.join(OUTPUT_DIR, 'orthogroups_fasta') - move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir) - write_html_output(out_file, title, orthogroups_fasta_dest_dir) + utils.move_directory_files(orthogroups_fasta_src_dir, orthogroups_fasta_dest_dir) + utils.write_html_output(out_file, title, orthogroups_fasta_dest_dir) # Handle single copy orthogroup outputs. if args.output_ptsco is not None: single_copy_fasta_src_dir = os.path.join(OUTPUT_DIR, 'single_copy_fasta') single_copy_fasta_dest_dir = args.output_ptsco_dir title = 'Single copy orthogroups files' - move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir) - write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir) + utils.move_directory_files(single_copy_fasta_src_dir, single_copy_fasta_dest_dir) + utils.write_html_output(args.output_ptsco, title, single_copy_fasta_dest_dir)