tmhmm_and_signalp: tools/protein_analysis/seq_analysis

annotate tools/protein_analysis/seq_analysis_utils.py @ 29:3cb02adf4326 draft

v0.2.9 Python style improvements

author	peterjc
date	Wed, 01 Feb 2017 09:46:14 -0500
parents	20139cb4c844
children	6d9d7cdf00fc

rev	line source
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	1 """A few useful functions for working with FASTA files and running jobs.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	2
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	3 This module was originally written to hold common code used in both the TMHMM
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	4 and SignalP wrappers in Galaxy.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	5
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	6 Given Galaxy currently supports Python 2.4+ this cannot use the Python module
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	7 multiprocessing so the function run_jobs instead is a simple pool approach
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	8 using just the subprocess library.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	9 """
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	10 import sys
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	11 import os
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	12 import subprocess
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	13 from time import sleep
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	14
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	15 __version__ = "0.0.2"
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	16
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	17 try:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	18 from multiprocessing import cpu_count
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	19 except ImportError:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	20 # Must be under Python 2.5, this is copied from multiprocessing:
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	21 def cpu_count():
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	22 """Returns the number of CPUs in the system."""
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	23 if sys.platform == 'win32':
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	24 try:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	25 num = int(os.environ['NUMBER_OF_PROCESSORS'])
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	26 except (ValueError, KeyError):
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	27 num = 0
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	28 elif 'bsd' in sys.platform or sys.platform == 'darwin':
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	29 comm = '/sbin/sysctl -n hw.ncpu'
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	30 if sys.platform == 'darwin':
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	31 comm = '/usr' + comm
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	32 try:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	33 with os.popen(comm) as p:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	34 num = int(p.read())
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	35 except ValueError:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	36 num = 0
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	37 else:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	38 try:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	39 num = os.sysconf('SC_NPROCESSORS_ONLN')
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	40 except (ValueError, OSError, AttributeError):
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	41 num = 0
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	42
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	43 if num >= 1:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	44 return num
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	45 else:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	46 raise NotImplementedError('cannot determine number of cpus')
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	47
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	48
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	49 def thread_count(command_line_arg, default=1):
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	50 try:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	51 num = int(command_line_arg)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	52 except ValueError:
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	53 num = default
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	54 if num < 1:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	55 sys.exit("Threads argument %r is not a positive integer" % command_line_arg)
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	56 # Cap this with the pysical limit of the machine,
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	57 try:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	58 num = min(num, cpu_count())
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	59 except NotImplementedError:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	60 pass
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	61 # For debugging,
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	62 # hostname = os.environ.get("HOSTNAME", "this machine")
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	63 # sys.stderr.write("Using %i cores on %s\n" % (num, hostname))
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	64 return num
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	65
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	66
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	67 def fasta_iterator(filename, max_len=None, truncate=None):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	68 """Simple FASTA parser yielding tuples of (title, sequence) strings."""
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	69 handle = open(filename)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	70 title, seq = "", ""
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	71 for line in handle:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	72 if line.startswith(">"):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	73 if title:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	74 if truncate:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	75 seq = seq[:truncate]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	76 if max_len and len(seq) > max_len:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	77 raise ValueError("Sequence %s is length %i, max length %i"
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	78 % (title.split()[0], len(seq), max_len))
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	79 yield title, seq
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	80 title = line[1:].rstrip()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	81 seq = ""
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82 elif title:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	83 seq += line.strip()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	84 elif not line.strip() or line.startswith("#"):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	85 # Ignore blank lines, and any comment lines
3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	86 # between records (starting with hash).
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	87 pass
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	88 else:
25 41a42022f815 Uploaded v0.2.6, embedded citations peterjc parents: 7 diff changeset	89 handle.close()
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	90 raise ValueError("Bad FASTA line %r" % line)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	91 handle.close()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	92 if title:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	93 if truncate:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	94 seq = seq[:truncate]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	95 if max_len and len(seq) > max_len:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	96 raise ValueError("Sequence %s is length %i, max length %i"
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	97 % (title.split()[0], len(seq), max_len))
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	98 yield title, seq
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	99 raise StopIteration
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	101
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	102 def split_fasta(input_filename, output_filename_base, n=500, truncate=None, keep_descr=False, max_len=None):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	103 """Split FASTA file into sub-files each of at most n sequences.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	104
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	105 Returns a list of the filenames used (based on the input filename).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106 Each sequence can also be truncated (since we only need the start for
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	107 SignalP), and have its description discarded (since we don't usually
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	108 care about it and some tools don't like very long title lines).
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	109
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	110 If a max_len is given and any sequence exceeds it no temp files are
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	111 created and an exception is raised.
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	112 """
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	113 iterator = fasta_iterator(input_filename, max_len, truncate)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	114 files = []
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	115 try:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	116 while True:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	117 records = []
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	118 for i in range(n):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	119 try:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	120 records.append(iterator.next())
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	121 except StopIteration:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	122 break
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	123 if not records:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	124 break
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	125 new_filename = "%s.%i.tmp" % (output_filename_base, len(files))
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	126 handle = open(new_filename, "w")
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	127 if keep_descr:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	128 for title, seq in records:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	129 handle.write(">%s\n" % title)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	130 for i in range(0, len(seq), 60):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	131 handle.write(seq[i:i + 60] + "\n")
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	132 else:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	133 for title, seq in records:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	134 handle.write(">%s\n" % title.split()[0])
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	135 for i in range(0, len(seq), 60):
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	136 handle.write(seq[i:i + 60] + "\n")
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	137 handle.close()
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	138 files.append(new_filename)
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	139 # print "%i records in %s" % (len(records), new_filename)
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	140 except ValueError, err:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	141 # Max length failure from parser - clean up
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	142 try:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	143 handle.close()
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	144 except Exception:
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	145 pass
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	146 for f in files:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	147 if os.path.isfile(f):
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	148 os.remove(f)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	149 raise err
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	150 for f in files:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	151 assert os.path.isfile(f), "Missing split file %r (!??)" % f
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	152 return files
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	153
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	154
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	155 def run_jobs(jobs, threads, pause=10, verbose=False):
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	156 """Takes list of cmd strings, returns dict with error levels."""
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	157 pending = jobs[:]
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	158 running = []
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	159 results = {}
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	160 if threads == 1:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	161 # Special case this for speed, don't need the waits
7 5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	162 for cmd in jobs:
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	163 results[cmd] = subprocess.call(cmd, shell=True)
5e62aefb2918 Uploaded v0.1.2 to Test Tool Shed peterjc parents: 6 diff changeset	164 return results
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	165 while pending or running:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	166 # See if any have finished
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	167 for (cmd, process) in running:
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	168 return_code = process.poll() # non-blocking
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	169 if return_code is not None:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	170 results[cmd] = return_code
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	171 running = [(cmd, process) for (cmd, process) in running
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	172 if cmd not in results]
3 fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	173 if verbose:
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	174 print "%i jobs pending, %i running, %i completed" \
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	175 % (len(pending), len(running), len(results))
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	176 # See if we can start any new threads
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	177 while pending and len(running) < threads:
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	178 cmd = pending.pop(0)
3 fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	179 if verbose:
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	180 print cmd
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	181 process = subprocess.Popen(cmd, shell=True)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	182 running.append((cmd, process))
29 3cb02adf4326 v0.2.9 Python style improvements peterjc parents: 26 diff changeset	183 # Loop...
6 39a6e46cdda3 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	184 sleep(pause)
3 fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	185 if verbose:
fe10f448d641 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	186 print "%i jobs completed" % len(results)
0 a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	187 assert set(jobs) == set(results)
a2eeeaa6f75e Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	188 return results

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/seq_analysis_utils.py @ 29:3cb02adf4326 draft