Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/seq_analysis_utils.py @ 14:6365217cd3de draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.2.3, adds unit tests for WoLF PSORT
author peterjc
date Thu, 25 Apr 2013 11:54:47 -0400
parents e52220a9ddad
children e6cc27d182a8
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rev   line source
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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
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22 try:
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23 from multiprocessing import cpu_count
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24 except ImportError:
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25 #Must be under Python 2.5, this is copied from multiprocessing:
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26 def cpu_count():
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27 """Returns the number of CPUs in the system."""
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28 if sys.platform == 'win32':
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29 try:
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30 num = int(os.environ['NUMBER_OF_PROCESSORS'])
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31 except (ValueError, KeyError):
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32 num = 0
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33 elif 'bsd' in sys.platform or sys.platform == 'darwin':
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34 comm = '/sbin/sysctl -n hw.ncpu'
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35 if sys.platform == 'darwin':
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36 comm = '/usr' + comm
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37 try:
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38 with os.popen(comm) as p:
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39 num = int(p.read())
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40 except ValueError:
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41 num = 0
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42 else:
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43 try:
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44 num = os.sysconf('SC_NPROCESSORS_ONLN')
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45 except (ValueError, OSError, AttributeError):
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46 num = 0
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47
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48 if num >= 1:
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49 return num
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50 else:
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51 raise NotImplementedError('cannot determine number of cpus')
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52
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53
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54 def thread_count(command_line_arg, default=1):
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55 try:
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56 num = int(command_line_arg)
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57 except:
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58 num = default
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59 if num < 1:
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60 stop_err("Threads argument %r is not a positive integer" % command_line_arg)
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61 #Cap this with the pysical limit of the machine,
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62 try:
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63 num = min(num, cpu_count())
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64 except NotImplementedError:
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65 pass
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66 #For debugging,
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67 #hostname = os.environ.get("HOSTNAME", "this machine")
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68 #sys.stderr.write("Using %i cores on %s\n" % (num, hostname))
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69 return num
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70
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71
0
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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
7
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153 for f in files:
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154 assert os.path.isfile(f), "Missing split file %r (!??)" % f
0
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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 = {}
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162 if threads == 1:
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163 #Special case this for speed, don't need the waits
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164 for cmd in jobs:
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165 results[cmd] = subprocess.call(cmd, shell=True)
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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