tmhmm_and_signalp: tools/protein_analysis/seq_analysis

annotate tools/protein_analysis/seq_analysis_utils.py @ 9:e52220a9ddad draft

Uploaded v0.1.2 Use the new <stdio> settings in the XML wrappers to catch errors. Obeys SGE style XNSLOTS environment variable for thread count (otherwise default to 4).

author	peterjc
date	Fri, 25 Jan 2013 06:08:31 -0500
parents	9b45a8743100
children	e6cc27d182a8

rev	line source
0 bca9bc7fdaef 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.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	2
bca9bc7fdaef 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
bca9bc7fdaef 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.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	5
bca9bc7fdaef 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
bca9bc7fdaef 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
bca9bc7fdaef 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.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	9 """
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	10 import sys
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	11 import os
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	12 import subprocess
bca9bc7fdaef 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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	14
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	15 __version__ = "0.0.1"
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	16
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	17 def stop_err(msg, error_level=1):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	18 """Print error message to stdout and quit with given error level."""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	19 sys.stderr.write("%s\n" % msg)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	20 sys.exit(error_level)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	21
9 e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	22 try:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	23 from multiprocessing import cpu_count
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	24 except ImportError:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	25 #Must be under Python 2.5, this is copied from multiprocessing:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	26 def cpu_count():
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	27 """Returns the number of CPUs in the system."""
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	28 if sys.platform == 'win32':
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	29 try:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	30 num = int(os.environ['NUMBER_OF_PROCESSORS'])
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	31 except (ValueError, KeyError):
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	32 num = 0
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	33 elif 'bsd' in sys.platform or sys.platform == 'darwin':
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	34 comm = '/sbin/sysctl -n hw.ncpu'
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	35 if sys.platform == 'darwin':
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	36 comm = '/usr' + comm
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	37 try:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	38 with os.popen(comm) as p:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	39 num = int(p.read())
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	40 except ValueError:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	41 num = 0
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	42 else:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	43 try:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	44 num = os.sysconf('SC_NPROCESSORS_ONLN')
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	45 except (ValueError, OSError, AttributeError):
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	46 num = 0
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	47
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	48 if num >= 1:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	49 return num
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	50 else:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	51 raise NotImplementedError('cannot determine number of cpus')
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	52
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	53
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	54 def thread_count(command_line_arg, default=1):
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	55 try:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	56 num = int(command_line_arg)
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	57 except:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	58 num = default
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	59 if num < 1:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	60 stop_err("Threads argument %r is not a positive integer" % command_line_arg)
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	61 #Cap this with the pysical limit of the machine,
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	62 try:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	63 num = min(num, cpu_count())
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	64 except NotImplementedError:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	65 pass
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	66 #For debugging,
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	67 #hostname = os.environ.get("HOSTNAME", "this machine")
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	68 #sys.stderr.write("Using %i cores on %s\n" % (num, hostname))
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	69 return num
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	70
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	71
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	72 def fasta_iterator(filename, max_len=None, truncate=None):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	73 """Simple FASTA parser yielding tuples of (title, sequence) strings."""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	74 handle = open(filename)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	75 title, seq = "", ""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	76 for line in handle:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	77 if line.startswith(">"):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	78 if title:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	79 if truncate:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	80 seq = seq[:truncate]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	81 if max_len and len(seq) > max_len:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	82 raise ValueError("Sequence %s is length %i, max length %i" \
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	83 % (title.split()[0], len(seq), max_len))
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	84 yield title, seq
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	85 title = line[1:].rstrip()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	86 seq = ""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	87 elif title:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	88 seq += line.strip()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	89 elif not line.strip() or line.startswith("#"):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	90 #Ignore blank lines, and any comment lines
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	91 #between records (starting with hash).
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	92 pass
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	93 else:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	94 raise ValueError("Bad FASTA line %r" % line)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	95 handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	96 if title:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	97 if truncate:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	98 seq = seq[:truncate]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	99 if max_len and len(seq) > max_len:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	100 raise ValueError("Sequence %s is length %i, max length %i" \
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	101 % (title.split()[0], len(seq), max_len))
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	102 yield title, seq
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	103 raise StopIteration
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	104
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	105 def split_fasta(input_filename, output_filename_base, n=500, truncate=None, keep_descr=False, max_len=None):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	106 """Split FASTA file into sub-files each of at most n sequences.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	107
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	108 Returns a list of the filenames used (based on the input filename).
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	109 Each sequence can also be truncated (since we only need the start for
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	110 SignalP), and have its description discarded (since we don't usually
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	111 care about it and some tools don't like very long title lines).
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	112
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	113 If a max_len is given and any sequence exceeds it no temp files are
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	114 created and an exception is raised.
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	115 """
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	116 iterator = fasta_iterator(input_filename, max_len, truncate)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	117 files = []
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	118 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	119 while True:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	120 records = []
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	121 for i in range(n):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	122 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	123 records.append(iterator.next())
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	124 except StopIteration:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	125 break
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	126 if not records:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	127 break
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	128 new_filename = "%s.%i.tmp" % (output_filename_base, len(files))
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	129 handle = open(new_filename, "w")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	130 if keep_descr:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	131 for title, seq in records:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	132 handle.write(">%s\n" % title)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	133 for i in range(0, len(seq), 60):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	134 handle.write(seq[i:i+60] + "\n")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	135 else:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	136 for title, seq in records:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	137 handle.write(">%s\n" % title.split()[0])
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	138 for i in range(0, len(seq), 60):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	139 handle.write(seq[i:i+60] + "\n")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	140 handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	141 files.append(new_filename)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	142 #print "%i records in %s" % (len(records), new_filename)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	143 except ValueError, err:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	144 #Max length failure from parser - clean up
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	145 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	146 handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	147 except:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	148 pass
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	149 for f in files:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	150 if os.path.isfile(f):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	151 os.remove(f)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	152 raise err
7 9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	153 for f in files:
9b45a8743100 Uploaded v0.1.0, which adds a wrapper for Promoter 2.0 (DNA tool) and enables use of Galaxy's <parallelism> tag for SignalP, TMHMM X Promoter wrappers. peterjc parents: 6 diff changeset	154 assert os.path.isfile(f), "Missing split file %r (!??)" % f
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	155 return files
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	156
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	157 def run_jobs(jobs, threads, pause=10, verbose=False):
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	158 """Takes list of cmd strings, returns dict with error levels."""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	159 pending = jobs[:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	160 running = []
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	161 results = {}
9 e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	162 if threads == 1:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	163 #Special case this for speed, don't need the waits
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	164 for cmd in jobs:
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	165 results[cmd] = subprocess.call(cmd, shell=True)
e52220a9ddad Uploaded v0.1.2 peterjc parents: 7 diff changeset	166 return results
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	167 while pending or running:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	168 #See if any have finished
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	169 for (cmd, process) in running:
3 f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	170 return_code = process.poll() #non-blocking
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	171 if return_code is not None:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	172 results[cmd] = return_code
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	173 running = [(cmd, process) for (cmd, process) in running \
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	174 if cmd not in results]
3 f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	175 if verbose:
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	176 print "%i jobs pending, %i running, %i completed" \
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	177 % (len(pending), len(running), len(results))
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	178 #See if we can start any new threads
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	179 while pending and len(running) < threads:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	180 cmd = pending.pop(0)
3 f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	181 if verbose:
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	182 print cmd
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	183 process = subprocess.Popen(cmd, shell=True)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	184 running.append((cmd, process))
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	185 #Loop...
6 a290c6d4e658 Migrated tool version 0.0.9 from old tool shed archive to new tool shed repository peterjc parents: 3 diff changeset	186 sleep(pause)
3 f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	187 if verbose:
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository peterjc parents: 0 diff changeset	188 print "%i jobs completed" % len(results)
0 bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	189 assert set(jobs) == set(results)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository peterjc parents: diff changeset	190 return results

Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/seq_analysis_utils.py @ 9:e52220a9ddad draft