Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/seq_analysis_utils.py @ 19:f3ecd80850e2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
v0.2.9 Python style improvements
author peterjc
date Wed, 01 Feb 2017 09:46:42 -0500
parents eb6ac44d4b8e
children a19b3ded8f33
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
15 __version__ = "0.0.2"
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
16
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
17 try:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
18 from multiprocessing import cpu_count
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
19 except ImportError:
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
20 # Must be under Python 2.5, this is copied from multiprocessing:
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
21 def cpu_count():
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
22 """Returns the number of CPUs in the system."""
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
23 if sys.platform == 'win32':
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
24 try:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
25 num = int(os.environ['NUMBER_OF_PROCESSORS'])
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
26 except (ValueError, KeyError):
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
27 num = 0
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
28 elif 'bsd' in sys.platform or sys.platform == 'darwin':
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
29 comm = '/sbin/sysctl -n hw.ncpu'
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
30 if sys.platform == 'darwin':
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
31 comm = '/usr' + comm
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
32 try:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
33 with os.popen(comm) as p:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
34 num = int(p.read())
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
35 except ValueError:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
36 num = 0
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
37 else:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
38 try:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
39 num = os.sysconf('SC_NPROCESSORS_ONLN')
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
40 except (ValueError, OSError, AttributeError):
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
41 num = 0
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
42
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
43 if num >= 1:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
44 return num
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
45 else:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
46 raise NotImplementedError('cannot determine number of cpus')
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
47
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
48
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
49 def thread_count(command_line_arg, default=1):
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
50 try:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
51 num = int(command_line_arg)
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
52 except ValueError:
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
53 num = default
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
54 if num < 1:
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
55 sys.exit("Threads argument %r is not a positive integer" % command_line_arg)
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
56 # Cap this with the pysical limit of the machine,
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
57 try:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
58 num = min(num, cpu_count())
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
59 except NotImplementedError:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
60 pass
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
61 # For debugging,
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
62 # hostname = os.environ.get("HOSTNAME", "this machine")
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
63 # sys.stderr.write("Using %i cores on %s\n" % (num, hostname))
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
64 return num
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
65
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
66
0
bca9bc7fdaef 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):
bca9bc7fdaef 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."""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
69 handle = open(filename)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
70 title, seq = "", ""
bca9bc7fdaef 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:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
72 if line.startswith(">"):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
73 if title:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
74 if truncate:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
75 seq = seq[:truncate]
bca9bc7fdaef 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:
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
77 raise ValueError("Sequence %s is length %i, max length %i"
0
bca9bc7fdaef 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))
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
79 yield title, seq
bca9bc7fdaef 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()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
81 seq = ""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
82 elif title:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
83 seq += line.strip()
bca9bc7fdaef 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("#"):
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
85 # Ignore blank lines, and any comment lines
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
86 # between records (starting with hash).
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
87 pass
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
88 else:
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
peterjc
parents: 9
diff changeset
89 handle.close()
0
bca9bc7fdaef 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)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
91 handle.close()
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
92 if title:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
93 if truncate:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
94 seq = seq[:truncate]
bca9bc7fdaef 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:
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
96 raise ValueError("Sequence %s is length %i, max length %i"
0
bca9bc7fdaef 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))
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
98 yield title, seq
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
99 raise StopIteration
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
100
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
101
0
bca9bc7fdaef 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):
bca9bc7fdaef 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.
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 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
106 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
107 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
108 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
109
bca9bc7fdaef 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
bca9bc7fdaef 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.
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 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
114 files = []
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
115 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
116 while True:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
117 records = []
bca9bc7fdaef 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):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
119 try:
bca9bc7fdaef 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())
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
121 except StopIteration:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
122 break
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
123 if not records:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
124 break
bca9bc7fdaef 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))
bca9bc7fdaef 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")
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
127 if keep_descr:
bca9bc7fdaef 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:
bca9bc7fdaef 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)
bca9bc7fdaef 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):
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
131 handle.write(seq[i:i + 60] + "\n")
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
132 else:
bca9bc7fdaef 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:
bca9bc7fdaef 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])
bca9bc7fdaef 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):
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
136 handle.write(seq[i:i + 60] + "\n")
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
137 handle.close()
bca9bc7fdaef 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)
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
139 # print "%i records in %s" % (len(records), new_filename)
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
140 except ValueError, err:
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
141 # Max length failure from parser - clean up
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
142 try:
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
143 handle.close()
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
144 except Exception:
0
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
145 pass
bca9bc7fdaef 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:
bca9bc7fdaef 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):
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
148 os.remove(f)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
149 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
150 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
151 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
152 return files
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
153
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
154
6
a290c6d4e658 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
bca9bc7fdaef 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."""
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
157 pending = jobs[:]
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
158 running = []
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
159 results = {}
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
160 if threads == 1:
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
161 # Special case this for speed, don't need the waits
9
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
162 for cmd in jobs:
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
163 results[cmd] = subprocess.call(cmd, shell=True)
e52220a9ddad Uploaded v0.1.2
peterjc
parents: 7
diff changeset
164 return results
0
bca9bc7fdaef 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:
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
166 # See if any have finished
0
bca9bc7fdaef 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:
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
168 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
169 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
170 results[cmd] = return_code
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
171 running = [(cmd, process) for (cmd, process) in running
0
bca9bc7fdaef 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
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
173 if verbose:
f3b373a41f81 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" \
f3b373a41f81 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))
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
176 # See if we can start any new threads
0
bca9bc7fdaef 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:
bca9bc7fdaef 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
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
179 if verbose:
f3b373a41f81 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
bca9bc7fdaef 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)
bca9bc7fdaef 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))
19
f3ecd80850e2 v0.2.9 Python style improvements
peterjc
parents: 18
diff changeset
183 # Loop...
6
a290c6d4e658 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
f3b373a41f81 Migrated tool version 0.0.6 from old tool shed archive to new tool shed repository
peterjc
parents: 0
diff changeset
185 if verbose:
f3b373a41f81 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
bca9bc7fdaef 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)
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
peterjc
parents:
diff changeset
188 return results