Mercurial > repos > peterjc > tmhmm_and_signalp
annotate tools/protein_analysis/seq_analysis_utils.py @ 16:7de64c8b258d draft
Uploaded v0.2.5, MIT licence, RST for README, citation information, development moved to GitHub
author | peterjc |
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date | Wed, 18 Sep 2013 06:16:58 -0400 |
parents | e52220a9ddad |
children | e6cc27d182a8 |
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1 """A few useful functions for working with FASTA files and running jobs. |
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2 |
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3 This module was originally written to hold common code used in both the TMHMM |
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4 and SignalP wrappers in Galaxy. |
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5 |
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6 Given Galaxy currently supports Python 2.4+ this cannot use the Python module |
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7 multiprocessing so the function run_jobs instead is a simple pool approach |
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8 using just the subprocess library. |
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9 """ |
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10 import sys |
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11 import os |
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12 import subprocess |
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13 from time import sleep |
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14 |
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15 __version__ = "0.0.1" |
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16 |
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17 def stop_err(msg, error_level=1): |
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18 """Print error message to stdout and quit with given error level.""" |
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19 sys.stderr.write("%s\n" % msg) |
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20 sys.exit(error_level) |
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21 |
9 | 22 try: |
23 from multiprocessing import cpu_count | |
24 except ImportError: | |
25 #Must be under Python 2.5, this is copied from multiprocessing: | |
26 def cpu_count(): | |
27 """Returns the number of CPUs in the system.""" | |
28 if sys.platform == 'win32': | |
29 try: | |
30 num = int(os.environ['NUMBER_OF_PROCESSORS']) | |
31 except (ValueError, KeyError): | |
32 num = 0 | |
33 elif 'bsd' in sys.platform or sys.platform == 'darwin': | |
34 comm = '/sbin/sysctl -n hw.ncpu' | |
35 if sys.platform == 'darwin': | |
36 comm = '/usr' + comm | |
37 try: | |
38 with os.popen(comm) as p: | |
39 num = int(p.read()) | |
40 except ValueError: | |
41 num = 0 | |
42 else: | |
43 try: | |
44 num = os.sysconf('SC_NPROCESSORS_ONLN') | |
45 except (ValueError, OSError, AttributeError): | |
46 num = 0 | |
47 | |
48 if num >= 1: | |
49 return num | |
50 else: | |
51 raise NotImplementedError('cannot determine number of cpus') | |
52 | |
53 | |
54 def thread_count(command_line_arg, default=1): | |
55 try: | |
56 num = int(command_line_arg) | |
57 except: | |
58 num = default | |
59 if num < 1: | |
60 stop_err("Threads argument %r is not a positive integer" % command_line_arg) | |
61 #Cap this with the pysical limit of the machine, | |
62 try: | |
63 num = min(num, cpu_count()) | |
64 except NotImplementedError: | |
65 pass | |
66 #For debugging, | |
67 #hostname = os.environ.get("HOSTNAME", "this machine") | |
68 #sys.stderr.write("Using %i cores on %s\n" % (num, hostname)) | |
69 return num | |
70 | |
71 | |
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72 def fasta_iterator(filename, max_len=None, truncate=None): |
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73 """Simple FASTA parser yielding tuples of (title, sequence) strings.""" |
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74 handle = open(filename) |
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75 title, seq = "", "" |
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76 for line in handle: |
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77 if line.startswith(">"): |
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78 if title: |
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79 if truncate: |
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80 seq = seq[:truncate] |
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81 if max_len and len(seq) > max_len: |
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82 raise ValueError("Sequence %s is length %i, max length %i" \ |
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83 % (title.split()[0], len(seq), max_len)) |
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84 yield title, seq |
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85 title = line[1:].rstrip() |
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86 seq = "" |
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87 elif title: |
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88 seq += line.strip() |
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89 elif not line.strip() or line.startswith("#"): |
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90 #Ignore blank lines, and any comment lines |
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91 #between records (starting with hash). |
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92 pass |
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93 else: |
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94 raise ValueError("Bad FASTA line %r" % line) |
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95 handle.close() |
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96 if title: |
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97 if truncate: |
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98 seq = seq[:truncate] |
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99 if max_len and len(seq) > max_len: |
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100 raise ValueError("Sequence %s is length %i, max length %i" \ |
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101 % (title.split()[0], len(seq), max_len)) |
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102 yield title, seq |
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103 raise StopIteration |
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104 |
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105 def split_fasta(input_filename, output_filename_base, n=500, truncate=None, keep_descr=False, max_len=None): |
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106 """Split FASTA file into sub-files each of at most n sequences. |
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107 |
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108 Returns a list of the filenames used (based on the input filename). |
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109 Each sequence can also be truncated (since we only need the start for |
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110 SignalP), and have its description discarded (since we don't usually |
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111 care about it and some tools don't like very long title lines). |
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112 |
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113 If a max_len is given and any sequence exceeds it no temp files are |
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114 created and an exception is raised. |
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115 """ |
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116 iterator = fasta_iterator(input_filename, max_len, truncate) |
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117 files = [] |
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118 try: |
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119 while True: |
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120 records = [] |
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121 for i in range(n): |
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122 try: |
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123 records.append(iterator.next()) |
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124 except StopIteration: |
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125 break |
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126 if not records: |
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127 break |
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128 new_filename = "%s.%i.tmp" % (output_filename_base, len(files)) |
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129 handle = open(new_filename, "w") |
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130 if keep_descr: |
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131 for title, seq in records: |
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132 handle.write(">%s\n" % title) |
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133 for i in range(0, len(seq), 60): |
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134 handle.write(seq[i:i+60] + "\n") |
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135 else: |
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136 for title, seq in records: |
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137 handle.write(">%s\n" % title.split()[0]) |
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138 for i in range(0, len(seq), 60): |
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139 handle.write(seq[i:i+60] + "\n") |
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140 handle.close() |
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141 files.append(new_filename) |
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142 #print "%i records in %s" % (len(records), new_filename) |
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143 except ValueError, err: |
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144 #Max length failure from parser - clean up |
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145 try: |
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146 handle.close() |
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147 except: |
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148 pass |
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149 for f in files: |
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150 if os.path.isfile(f): |
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151 os.remove(f) |
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152 raise err |
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153 for f in files: |
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154 assert os.path.isfile(f), "Missing split file %r (!??)" % f |
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155 return files |
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156 |
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157 def run_jobs(jobs, threads, pause=10, verbose=False): |
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158 """Takes list of cmd strings, returns dict with error levels.""" |
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159 pending = jobs[:] |
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160 running = [] |
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161 results = {} |
9 | 162 if threads == 1: |
163 #Special case this for speed, don't need the waits | |
164 for cmd in jobs: | |
165 results[cmd] = subprocess.call(cmd, shell=True) | |
166 return results | |
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167 while pending or running: |
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168 #See if any have finished |
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169 for (cmd, process) in running: |
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170 return_code = process.poll() #non-blocking |
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171 if return_code is not None: |
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172 results[cmd] = return_code |
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173 running = [(cmd, process) for (cmd, process) in running \ |
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174 if cmd not in results] |
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175 if verbose: |
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176 print "%i jobs pending, %i running, %i completed" \ |
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177 % (len(pending), len(running), len(results)) |
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178 #See if we can start any new threads |
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179 while pending and len(running) < threads: |
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180 cmd = pending.pop(0) |
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181 if verbose: |
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182 print cmd |
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183 process = subprocess.Popen(cmd, shell=True) |
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184 running.append((cmd, process)) |
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185 #Loop... |
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186 sleep(pause) |
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187 if verbose: |
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188 print "%i jobs completed" % len(results) |
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189 assert set(jobs) == set(results) |
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190 return results |