Mercurial > repos > peterjc > tmhmm_and_signalp

annotate tools/protein_analysis/seq_analysis_utils.py @ 17:e6cc27d182a8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
author peterjc
date Fri, 21 Nov 2014 08:19:09 -0500
parents e52220a9ddad
children eb6ac44d4b8e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
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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
bca9bc7fdaef Migrated tool version 0.0.1 from old tool shed archive to new tool shed repository
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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:
17
e6cc27d182a8 Uploaded v0.2.6, embedded citations and uses $GALAXY_SLOTS
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94 handle.close()
0
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95 raise ValueError("Bad FASTA line %r" % line)
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96 handle.close()
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97 if title:
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98 if truncate:
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99 seq = seq[:truncate]
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100 if max_len and len(seq) > max_len:
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101 raise ValueError("Sequence %s is length %i, max length %i" \
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102 % (title.split()[0], len(seq), max_len))
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103 yield title, seq
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104 raise StopIteration
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105
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106 def split_fasta(input_filename, output_filename_base, n=500, truncate=None, keep_descr=False, max_len=None):
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107 """Split FASTA file into sub-files each of at most n sequences.
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108
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109 Returns a list of the filenames used (based on the input filename).
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110 Each sequence can also be truncated (since we only need the start for
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111 SignalP), and have its description discarded (since we don't usually
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112 care about it and some tools don't like very long title lines).
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113
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114 If a max_len is given and any sequence exceeds it no temp files are
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115 created and an exception is raised.
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116 """
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117 iterator = fasta_iterator(input_filename, max_len, truncate)
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118 files = []
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119 try:
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120 while True:
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121 records = []
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122 for i in range(n):
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123 try:
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124 records.append(iterator.next())
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125 except StopIteration:
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126 break
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127 if not records:
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128 break
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129 new_filename = "%s.%i.tmp" % (output_filename_base, len(files))
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130 handle = open(new_filename, "w")
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131 if keep_descr:
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132 for title, seq in records:
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133 handle.write(">%s\n" % title)
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134 for i in range(0, len(seq), 60):
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135 handle.write(seq[i:i+60] + "\n")
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136 else:
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137 for title, seq in records:
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138 handle.write(">%s\n" % title.split()[0])
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139 for i in range(0, len(seq), 60):
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140 handle.write(seq[i:i+60] + "\n")
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141 handle.close()
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142 files.append(new_filename)
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143 #print "%i records in %s" % (len(records), new_filename)
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144 except ValueError, err:
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145 #Max length failure from parser - clean up
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146 try:
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147 handle.close()
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148 except:
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149 pass
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150 for f in files:
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151 if os.path.isfile(f):
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152 os.remove(f)
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153 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.
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154 for f in files:
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155 assert os.path.isfile(f), "Missing split file %r (!??)" % f
0
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156 return files
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157
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158 def run_jobs(jobs, threads, pause=10, verbose=False):
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159 """Takes list of cmd strings, returns dict with error levels."""
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160 pending = jobs[:]
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161 running = []
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162 results = {}
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163 if threads == 1:
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164 #Special case this for speed, don't need the waits
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165 for cmd in jobs:
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166 results[cmd] = subprocess.call(cmd, shell=True)
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167 return results
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168 while pending or running:
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169 #See if any have finished
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170 for (cmd, process) in running:
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171 return_code = process.poll() #non-blocking
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172 if return_code is not None:
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173 results[cmd] = return_code
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174 running = [(cmd, process) for (cmd, process) in running \
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175 if cmd not in results]
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176 if verbose:
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177 print "%i jobs pending, %i running, %i completed" \
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178 % (len(pending), len(running), len(results))
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179 #See if we can start any new threads
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180 while pending and len(running) < threads:
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181 cmd = pending.pop(0)
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182 if verbose:
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183 print cmd
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184 process = subprocess.Popen(cmd, shell=True)
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185 running.append((cmd, process))
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186 #Loop...
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187 sleep(pause)
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188 if verbose:
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189 print "%i jobs completed" % len(results)
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190 assert set(jobs) == set(results)
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191 return results