Mercurial > repos > peterjc > effectivet3

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit d67596914a7bbe183851437eaafe8c7305877e5a-dirty
author peterjc
date Fri, 22 Feb 2019 10:13:22 -0500
parents 011cfce866f1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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2 """Wrapper for EffectiveT3 v1.0.1 for use in Galaxy.
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3
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4 This script takes exactly five command line arguments:
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5 * model name (e.g. TTSS_STD-1.0.1.jar)
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6 * threshold (selective or sensitive)
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7 * an input protein FASTA filename
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8 * output tabular filename
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9
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10 It then calls the standalone Effective T3 v1.0.1 program (not the
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11 webservice), and reformats the semi-colon separated output into
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12 tab separated output for use in Galaxy.
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13 """
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14 import os
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16 # We want to be able to use shutil.which, but need Python 3.3+
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17 # import shutil
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18 import subprocess
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19 import sys
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21 # The Galaxy auto-install via tool_dependencies.xml will set the
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22 # environment variable $EFFECTIVET3 pointing at the folder with
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23 # the JAR file.
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24 #
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25 # The BioConda recipe will put a wrapper script on the $PATH,
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26 # which we can use to find the JAR file.
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27 #
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28 # We fall back on /opt/EffectiveT3/
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29 #
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30 effective_t3_jarname = "TTSS_GUI-1.0.1.jar"
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32 if "-v" in sys.argv or "--version" in sys.argv:
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33 # TODO - Get version of the JAR file dynamically?
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34 print("Wrapper v0.0.20, for %s" % effective_t3_jarname)
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35 sys.exit(0)
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36
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37 if len(sys.argv) != 5:
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38 sys.exit(
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39 "Require four arguments: model, threshold, input protein "
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40 "FASTA file & output tabular file"
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41 )
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43 model, threshold, fasta_file, tabular_file = sys.argv[1:]
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44
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45 if not os.path.isfile(fasta_file):
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46 sys.exit("Input FASTA file not found: %s" % fasta_file)
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47
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48 if threshold not in ["selective", "sensitive"] and not threshold.startswith("cutoff="):
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49 sys.exit(
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50 "Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold
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51 )
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54 def clean_tabular(raw_handle, out_handle):
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55 """Clean up Effective T3 output to make it tabular."""
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56 count = 0
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57 positive = 0
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58 errors = 0
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59 for line in raw_handle:
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60 if (
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61 not line
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62 or line.startswith("#")
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63 or line.startswith("Id; Description; Score;")
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64 ):
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65 continue
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66 assert line.count(";") >= 3, repr(line)
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67 # Normally there will just be three semi-colons, however the
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68 # original FASTA file's ID or description might have had
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69 # semi-colons in it as well, hence the following hackery:
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70 try:
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71 id_descr, score, effective = line.rstrip("\r\n").rsplit(";", 2)
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72 # Cope when there was no FASTA description
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73 if "; " not in id_descr and id_descr.endswith(";"):
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74 id = id_descr[:-1]
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75 descr = ""
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76 else:
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77 id, descr = id_descr.split("; ", 1)
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78 except ValueError:
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79 sys.exit("Problem parsing line:\n%s\n" % line)
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80 parts = [s.strip() for s in [id, descr, score, effective]]
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81 out_handle.write("\t".join(parts) + "\n")
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82 count += 1
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83 if float(score) < 0:
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84 errors += 1
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85 if effective.lower() == "true":
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86 positive += 1
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87 return count, positive, errors
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88
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89
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90 def run(cmd):
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91 """Run the command line string via subprocess."""
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92 # Avoid using shell=True when we call subprocess to ensure if the Python
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93 # script is killed, so too is the child process.
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94 try:
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95 child = subprocess.Popen(
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96 cmd, universal_newlines=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE
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97 )
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98 except Exception as err:
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99 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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100 # Use .communicate as can get deadlocks with .wait(),
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101 stdout, stderr = child.communicate()
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102 return_code = child.returncode
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103 if return_code or stderr.startswith("Exception in thread"):
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104 cmd_str = " ".join(cmd) # doesn't quote spaces etc
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105 if stderr and stdout:
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106 sys.exit(
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107 "Return code %i from command:\n%s\n\n%s\n\n%s"
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108 % (return_code, cmd_str, stdout, stderr)
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109 )
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110 else:
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111 sys.exit(
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112 "Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)
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113 )
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114
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115
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116 try:
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117 from shutil import which
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118 except ImportError:
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119 # Likely running on Python 2, use backport:
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120 def which(cmd, mode=os.F_OK | os.X_OK, path=None):
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121 """Python implementation of command line tool which.
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122
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123 Given a command, mode, and a PATH string, return the path which
32
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124 conforms to the given mode on the PATH, or None if there is no such
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125 file.
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126
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127 `mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result
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128 of os.environ.get("PATH"), or can be overridden with a custom search
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129 path.
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130 """
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131 # Check that a given file can be accessed with the correct mode.
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132 # Additionally check that `file` is not a directory, as on Windows
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133 # directories pass the os.access check.
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134 def _access_check(fn, mode):
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135 return os.path.exists(fn) and os.access(fn, mode) and not os.path.isdir(fn)
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136
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137 # Short circuit. If we're given a full path which matches the mode
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138 # and it exists, we're done here.
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139 if _access_check(cmd, mode):
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140 return cmd
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141
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142 path = (path or os.environ.get("PATH", os.defpath)).split(os.pathsep)
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143
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144 if sys.platform == "win32":
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145 # The current directory takes precedence on Windows.
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146 if os.curdir not in path:
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147 path.insert(0, os.curdir)
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148
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149 # PATHEXT is necessary to check on Windows.
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150 pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
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151 # See if the given file matches any of the expected path extensions.
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152 # This will allow us to short circuit when given "python.exe".
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153 matches = [cmd for ext in pathext if cmd.lower().endswith(ext.lower())]
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154 # If it does match, only test that one, otherwise we have to try
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155 # others.
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156 files = [cmd] if matches else [cmd + ext.lower() for ext in pathext]
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157 else:
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158 # On other platforms you don't have things like PATHEXT to tell you
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159 # what file suffixes are executable, so just pass on cmd as-is.
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160 files = [cmd]
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161
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162 seen = set()
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163 for dir in path:
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164 dir = os.path.normcase(dir)
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165 if dir not in seen:
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166 seen.add(dir)
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167 for thefile in files:
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168 name = os.path.join(dir, thefile)
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169 if _access_check(name, mode):
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170 return name
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171 return None
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172
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173
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174 # Try in order the following to find the JAR file:
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175 # - Location of any wrapper script, e.g. from BioConda installation
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176 # - The $EFFECTIVET3 env var, e.g. old-style Galaxy tool installation
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177 # - The /opt/EffectiveT3/ folder.
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178 effective_t3_jar = None
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179 effective_t3_dir = None
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180 dirs = ["/opt/EffectiveT3/"]
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181 if "EFFECTIVET3" in os.environ:
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182 dirs.insert(0, os.environ.get("EFFECTIVET3"))
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183 if which("effectivet3"):
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184 # Assuming this is a BioConda installed wrapper for effective T3,
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185 # this will get the directory of the wrapper script which is where
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186 # the JAR file will be:
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187 dirs.insert(0, os.path.split(os.path.realpath(which("effectivet3")))[0])
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188 for effective_t3_dir in dirs:
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189 effective_t3_jar = os.path.join(effective_t3_dir, effective_t3_jarname)
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190 if os.path.isfile(effective_t3_jar):
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191 # Good
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192 break
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193 effective_t3_jar = None
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194 if not effective_t3_dir or not effective_t3_jar:
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195 sys.exit("Effective T3 JAR file %r not found in %r" % (effective_t3_jarname, dirs))
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196
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197 if not os.path.isdir(os.path.join(effective_t3_dir, "module")):
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198 sys.exit(
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199 "Effective T3 module folder not found: %r"
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200 % os.path.join(effective_t3_dir, "module")
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201 )
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202
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203 effective_t3_model = os.path.join(effective_t3_dir, "module", model)
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204 if not os.path.isfile(effective_t3_model):
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205 sys.stderr.write(
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206 "Contents of %r is %s\n"
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207 % (
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208 os.path.join(effective_t3_dir, "module"),
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209 ", ".join(
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210 repr(p) for p in os.listdir(os.path.join(effective_t3_dir, "module"))
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211 ),
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212 )
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213 )
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214 sys.stderr.write("Main JAR was found: %r\n" % effective_t3_jar)
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215 sys.exit("Effective T3 model JAR file not found: %r" % effective_t3_model)
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216
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217 # We will have write access wherever the output should be,
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218 if tabular_file == "/dev/stdout":
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219 temp_file = os.path.abspath("effectivet3_tabular_output.tmp")
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220 else:
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221 temp_file = os.path.abspath(tabular_file + ".tmp")
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222
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223 # Use absolute paths since will change current directory...
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224 tabular_file = os.path.abspath(tabular_file)
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225 fasta_file = os.path.abspath(fasta_file)
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226
35
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227 cmd = [
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228 "java",
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229 "-jar",
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230 effective_t3_jar,
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231 "-f",
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232 fasta_file,
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233 "-m",
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234 model,
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235 "-t",
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236 threshold,
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237 "-o",
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238 temp_file,
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239 "-q",
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240 ]
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241
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242 try:
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243 # Must run from directory above the module subfolder:
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244 os.chdir(effective_t3_dir)
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245 except Exception:
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246 sys.exit("Could not change to Effective T3 folder: %s" % effective_t3_dir)
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247
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248 run(cmd)
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249
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250 if not os.path.isfile(temp_file):
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251 sys.exit("ERROR - No output file from Effective T3")
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252
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253 out_handle = open(tabular_file, "w")
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254 out_handle.write("#ID\tDescription\tScore\tEffective\n")
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255 data_handle = open(temp_file)
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256 count, positive, errors = clean_tabular(data_handle, out_handle)
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257 data_handle.close()
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258 out_handle.close()
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259
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260 os.remove(temp_file)
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261
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262 if errors:
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263 print("%i sequences, %i positive, %i errors" % (count, positive, errors))
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264 else:
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265 print("%i/%i sequences positive" % (positive, count))
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266
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267 if count and count == errors:
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268 # Galaxy will still allow them to see the output file
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269 sys.exit("All your sequences gave an error code")