Mercurial > repos > peterjc > effectivet3

annotate tools/effectiveT3/effectiveT3.py @ 32:1129cafdf0ae draft

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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
author peterjc
date Wed, 07 Jun 2017 10:51:31 -0400
parents 3ef6c246ccac
children 011cfce866f1
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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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15 # We want to be able to use shutil.which, but need Python 3.3+
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16 # import shutil
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17 import subprocess
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18 import sys
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20 # The Galaxy auto-install via tool_dependencies.xml will set the
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21 # environment variable $EFFECTIVET3 pointing at the folder with
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22 # the JAR file.
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23 #
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24 # The BioConda recipe will put a wrapper script on the $PATH,
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25 # which we can use to find the JAR file.
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26 #
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27 # We fall back on /opt/EffectiveT3/
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28 #
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29 effective_t3_jarname = "TTSS_GUI-1.0.1.jar"
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31 if "-v" in sys.argv or "--version" in sys.argv:
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32 # TODO - Get version of the JAR file dynamically?
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33 print("Wrapper v0.0.20, for %s" % effective_t3_jarname)
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34 sys.exit(0)
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35
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36 if len(sys.argv) != 5:
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37 sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
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39 model, threshold, fasta_file, tabular_file = sys.argv[1:]
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40
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41 if not os.path.isfile(fasta_file):
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42 sys.exit("Input FASTA file not found: %s" % fasta_file)
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44 if threshold not in ["selective", "sensitive"] and not threshold.startswith("cutoff="):
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45 sys.exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
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46
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48 def clean_tabular(raw_handle, out_handle):
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49 """Clean up Effective T3 output to make it tabular."""
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50 count = 0
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51 positive = 0
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52 errors = 0
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53 for line in raw_handle:
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54 if not line or line.startswith("#") or line.startswith("Id; Description; Score;"):
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55 continue
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56 assert line.count(";") >= 3, repr(line)
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57 # Normally there will just be three semi-colons, however the
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58 # original FASTA file's ID or description might have had
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59 # semi-colons in it as well, hence the following hackery:
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60 try:
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61 id_descr, score, effective = line.rstrip("\r\n").rsplit(";", 2)
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62 # Cope when there was no FASTA description
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63 if "; " not in id_descr and id_descr.endswith(";"):
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64 id = id_descr[:-1]
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65 descr = ""
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66 else:
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67 id, descr = id_descr.split("; ", 1)
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68 except ValueError:
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69 sys.exit("Problem parsing line:\n%s\n" % line)
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70 parts = [s.strip() for s in [id, descr, score, effective]]
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71 out_handle.write("\t".join(parts) + "\n")
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72 count += 1
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73 if float(score) < 0:
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74 errors += 1
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75 if effective.lower() == "true":
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76 positive += 1
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77 return count, positive, errors
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78
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79
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80 def run(cmd):
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81 """Run the command line string via subprocess."""
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82 # Avoid using shell=True when we call subprocess to ensure if the Python
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83 # script is killed, so too is the child process.
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84 try:
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85 child = subprocess.Popen(cmd, universal_newlines=True,
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86 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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87 except Exception as err:
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88 sys.exit("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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89 # Use .communicate as can get deadlocks with .wait(),
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90 stdout, stderr = child.communicate()
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91 return_code = child.returncode
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92 if return_code or stderr.startswith("Exception in thread"):
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93 cmd_str = " ".join(cmd) # doesn't quote spaces etc
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94 if stderr and stdout:
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95 sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr))
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96 else:
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97 sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr))
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98
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99
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100 try:
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101 from shutil import which
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102 except ImportError:
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103 # Likely running on Python 2, use backport:
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104 def which(cmd, mode=os.F_OK | os.X_OK, path=None):
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105 """Given a command, mode, and a PATH string, return the path which
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106 conforms to the given mode on the PATH, or None if there is no such
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107 file.
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108 `mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result
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109 of os.environ.get("PATH"), or can be overridden with a custom search
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110 path.
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111 """
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112
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113 # Check that a given file can be accessed with the correct mode.
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114 # Additionally check that `file` is not a directory, as on Windows
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115 # directories pass the os.access check.
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116 def _access_check(fn, mode):
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117 return (os.path.exists(fn) and os.access(fn, mode) and
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118 not os.path.isdir(fn))
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119
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120 # Short circuit. If we're given a full path which matches the mode
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121 # and it exists, we're done here.
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122 if _access_check(cmd, mode):
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123 return cmd
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124
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125 path = (path or os.environ.get("PATH", os.defpath)).split(os.pathsep)
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126
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127 if sys.platform == "win32":
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128 # The current directory takes precedence on Windows.
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129 if os.curdir not in path:
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130 path.insert(0, os.curdir)
2
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131
32
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132 # PATHEXT is necessary to check on Windows.
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133 pathext = os.environ.get("PATHEXT", "").split(os.pathsep)
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134 # See if the given file matches any of the expected path extensions.
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135 # This will allow us to short circuit when given "python.exe".
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136 matches = [cmd for ext in pathext if cmd.lower().endswith(ext.lower())]
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137 # If it does match, only test that one, otherwise we have to try
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138 # others.
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139 files = [cmd] if matches else [cmd + ext.lower() for ext in pathext]
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140 else:
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141 # On other platforms you don't have things like PATHEXT to tell you
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142 # what file suffixes are executable, so just pass on cmd as-is.
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143 files = [cmd]
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144
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145 seen = set()
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146 for dir in path:
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147 dir = os.path.normcase(dir)
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148 if dir not in seen:
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149 seen.add(dir)
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150 for thefile in files:
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151 name = os.path.join(dir, thefile)
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152 if _access_check(name, mode):
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153 return name
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154 return None
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155
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156
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157 # Try in order the following to find the JAR file:
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158 # - Location of any wrapper script, e.g. from BioConda installation
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159 # - The $EFFECTIVET3 env var, e.g. old-style Galaxy tool installation
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160 # - The /opt/EffectiveT3/ folder.
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161 effective_t3_jar = None
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162 effective_t3_dir = None
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163 dirs = ["/opt/EffectiveT3/"]
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164 if "EFFECTIVET3" in os.environ:
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165 dirs.insert(0, os.environ.get("EFFECTIVET3"))
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166 if which("effectivet3"):
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167 # Assuming this is a BioConda installed wrapper for effective T3,
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168 # this will get the directory of the wrapper script which is where
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169 # the JAR file will be:
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170 dirs.insert(0, os.path.split(os.path.realpath(which("effectivet3")))[0])
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171 for effective_t3_dir in dirs:
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172 effective_t3_jar = os.path.join(effective_t3_dir, effective_t3_jarname)
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173 if os.path.isfile(effective_t3_jar):
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174 # Good
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175 break
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176 effective_t3_jar = None
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177 if not effective_t3_dir or not effective_t3_jar:
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178 sys.exit("Effective T3 JAR file %r not found in %r" % (effective_t3_jarname, dirs))
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179
23
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180 if not os.path.isdir(os.path.join(effective_t3_dir, "module")):
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181 sys.exit("Effective T3 module folder not found: %r" % os.path.join(effective_t3_dir, "module"))
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182
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183 effective_t3_model = os.path.join(effective_t3_dir, "module", model)
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184 if not os.path.isfile(effective_t3_model):
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185 sys.stderr.write("Contents of %r is %s\n"
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186 % (os.path.join(effective_t3_dir, "module"),
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187 ", ".join(repr(p) for p in os.listdir(os.path.join(effective_t3_dir, "module")))))
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188 sys.stderr.write("Main JAR was found: %r\n" % effective_t3_jar)
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189 sys.exit("Effective T3 model JAR file not found: %r" % effective_t3_model)
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190
30
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191 # We will have write access wherever the output should be,
32
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192 if tabular_file == "/dev/stdout":
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193 temp_file = os.path.abspath("effectivet3_tabular_output.tmp")
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194 else:
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195 temp_file = os.path.abspath(tabular_file + ".tmp")
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196
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197 # Use absolute paths since will change current directory...
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198 tabular_file = os.path.abspath(tabular_file)
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199 fasta_file = os.path.abspath(fasta_file)
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200
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201 cmd = ["java", "-jar", effective_t3_jar,
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202 "-f", fasta_file,
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203 "-m", model,
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204 "-t", threshold,
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205 "-o", temp_file,
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206 "-q"]
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207
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208 try:
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209 # Must run from directory above the module subfolder:
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210 os.chdir(effective_t3_dir)
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211 except Exception:
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212 sys.exit("Could not change to Effective T3 folder: %s" % effective_t3_dir)
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213
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214 run(cmd)
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215
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216 if not os.path.isfile(temp_file):
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217 sys.exit("ERROR - No output file from Effective T3")
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218
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219 out_handle = open(tabular_file, "w")
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220 out_handle.write("#ID\tDescription\tScore\tEffective\n")
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221 data_handle = open(temp_file)
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222 count, positive, errors = clean_tabular(data_handle, out_handle)
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223 data_handle.close()
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224 out_handle.close()
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225
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226 os.remove(temp_file)
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227
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228 if errors:
23
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229 print("%i sequences, %i positive, %i errors"
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230 % (count, positive, errors))
2
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231 else:
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232 print("%i/%i sequences positive" % (positive, count))
2
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233
23
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234 if count and count == errors:
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235 # Galaxy will still allow them to see the output file
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236 sys.exit("All your sequences gave an error code")