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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 sys
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15 import os
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16 import subprocess
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17
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18 #The Galaxy auto-install via tool_dependencies.xml will set this environment variable
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19 effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/")
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20 effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar")
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21
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22 if "-v" in sys.argv or "--version" in sys.argv:
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23 #TODO - Get version of the JAR file dynamically?
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24 print "Wrapper v0.0.11, TTSS_GUI-1.0.1.jar"
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25 sys.exit(0)
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26
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27 def stop_err(msg, error_level=1):
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28 """Print error message to stdout and quit with given error level."""
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29 sys.stderr.write("%s\n" % msg)
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30 sys.exit(error_level)
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31
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32 if len(sys.argv) != 5:
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33 stop_err("Require four arguments: model, threshold, input protein FASTA file & output tabular file")
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34
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35 model, threshold, fasta_file, tabular_file = sys.argv[1:]
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36
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37 if not os.path.isfile(fasta_file):
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38 stop_err("Input FASTA file not found: %s" % fasta_file)
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39
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40 if threshold not in ["selective", "sensitive"] \
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41 and not threshold.startswith("cutoff="):
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42 stop_err("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold)
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43
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44 def clean_tabular(raw_handle, out_handle):
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45 """Clean up Effective T3 output to make it tabular."""
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46 count = 0
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47 positive = 0
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48 errors = 0
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49 for line in raw_handle:
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50 if not line or line.startswith("#") \
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51 or line.startswith("Id; Description; Score;"):
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52 continue
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53 assert line.count(";") >= 3, repr(line)
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54 #Normally there will just be three semi-colons, however the
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55 #original FASTA file's ID or description might have had
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56 #semi-colons in it as well, hence the following hackery:
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57 try:
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58 id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2)
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59 #Cope when there was no FASTA description
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60 if "; " not in id_descr and id_descr.endswith(";"):
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61 id = id_descr[:-1]
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62 descr = ""
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63 else:
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64 id, descr = id_descr.split("; ",1)
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65 except ValueError:
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66 stop_err("Problem parsing line:\n%s\n" % line)
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67 parts = [s.strip() for s in [id, descr, score, effective]]
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68 out_handle.write("\t".join(parts) + "\n")
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69 count += 1
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70 if float(score) < 0:
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71 errors += 1
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72 if effective.lower() == "true":
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73 positive += 1
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74 return count, positive, errors
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75
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76 def run(cmd):
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77 #Avoid using shell=True when we call subprocess to ensure if the Python
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78 #script is killed, so too is the child process.
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79 try:
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80 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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81 except Exception, err:
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82 stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
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83 #Use .communicate as can get deadlocks with .wait(),
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84 stdout, stderr = child.communicate()
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85 return_code = child.returncode
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86 if return_code:
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87 if stderr and stdout:
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88 stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr))
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89 else:
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90 stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr))
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91
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92 if not os.path.isdir(effectiveT3_dir):
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93 stop_err("Effective T3 folder not found: %s" % effectiveT3_dir)
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94
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95 if not os.path.isfile(effectiveT3_jar):
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96 stop_err("Effective T3 JAR file not found: %s" % effectiveT3_jar)
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97
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98 effectiveT3_model = os.path.join(effectiveT3_dir, "module", model)
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99 if not os.path.isfile(effectiveT3_model):
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100 stop_err("Effective T3 model JAR file not found: %s" % effectiveT3_model)
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101
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102 #We will have write access whereever the output should be,
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103 temp_file = os.path.abspath(tabular_file + ".tmp")
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104
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105 #Use absolute paths since will change current directory...
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106 tabular_file = os.path.abspath(tabular_file)
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107 fasta_file = os.path.abspath(fasta_file)
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108
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109 cmd = ["java", "-jar", effectiveT3_jar,
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110 "-f", fasta_file,
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111 "-m", model,
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112 "-t", threshold,
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113 "-o", temp_file,
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114 "-q"]
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115
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116 try:
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117 #Must run from directory above the module subfolder:
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118 os.chdir(effectiveT3_dir)
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119 except:
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120 stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir)
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121
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122 run(cmd)
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123
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124 if not os.path.isfile(temp_file):
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125 stop_err("ERROR - No output file from Effective T3")
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126
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127 out_handle = open(tabular_file, "w")
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128 out_handle.write("#ID\tDescription\tScore\tEffective\n")
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129 data_handle = open(temp_file)
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130 count, positive, errors = clean_tabular(data_handle, out_handle)
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131 data_handle.close()
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132 out_handle.close()
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133
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134 os.remove(temp_file)
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135
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136 if errors:
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137 print "%i sequences, %i positive, %i errors" \
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138 % (count, positive, errors)
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139 else:
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140 print "%i/%i sequences positive" % (positive, count)
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141
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142 if count and count==errors:
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143 #Galaxy will still allow them to see the output file
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144 stop_err("All your sequences gave an error code")
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