Mercurial > repos > peterjc > effectivet3
annotate tools/effectiveT3/effectiveT3.py @ 5:1ea715da1879 draft
Uploaded v0.0.13, embed citation, relax test for floating point differences
author | peterjc |
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date | Tue, 25 Nov 2014 08:28:24 -0500 |
parents | b0b927299aee |
children | 0f6eb4a75000 |
rev | line source |
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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 v0.0.13, 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 cmd_str= " ".join(cmd) # doesn't quote spaces etc |
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88 if stderr and stdout: |
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89 stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) |
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90 else: |
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91 stop_err("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) |
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92 |
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93 if not os.path.isdir(effectiveT3_dir): |
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94 stop_err("Effective T3 folder not found: %r" % effectiveT3_dir) |
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95 |
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96 if not os.path.isfile(effectiveT3_jar): |
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97 stop_err("Effective T3 JAR file not found: %r" % effectiveT3_jar) |
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98 |
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99 if not os.path.isdir(os.path.join(effectiveT3_dir, "module")): |
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100 stop_err("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module")) |
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101 |
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102 effectiveT3_model = os.path.join(effectiveT3_dir, "module", model) |
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103 if not os.path.isfile(effectiveT3_model): |
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104 sys.stderr.write("Contents of %r is %s\n" |
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105 % (os.path.join(effectiveT3_dir, "module"), |
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106 ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module"))))) |
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107 sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar) |
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108 stop_err("Effective T3 model JAR file not found: %r" % effectiveT3_model) |
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109 |
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110 # We will have write access whereever the output should be, |
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111 temp_file = os.path.abspath(tabular_file + ".tmp") |
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112 |
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113 # Use absolute paths since will change current directory... |
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114 tabular_file = os.path.abspath(tabular_file) |
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115 fasta_file = os.path.abspath(fasta_file) |
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116 |
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117 cmd = ["java", "-jar", effectiveT3_jar, |
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118 "-f", fasta_file, |
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119 "-m", model, |
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120 "-t", threshold, |
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121 "-o", temp_file, |
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122 "-q"] |
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123 |
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124 try: |
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125 # Must run from directory above the module subfolder: |
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126 os.chdir(effectiveT3_dir) |
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127 except: |
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128 stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir) |
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129 |
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130 run(cmd) |
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131 |
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132 if not os.path.isfile(temp_file): |
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133 stop_err("ERROR - No output file from Effective T3") |
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134 |
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135 out_handle = open(tabular_file, "w") |
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136 out_handle.write("#ID\tDescription\tScore\tEffective\n") |
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137 data_handle = open(temp_file) |
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138 count, positive, errors = clean_tabular(data_handle, out_handle) |
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139 data_handle.close() |
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140 out_handle.close() |
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141 |
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142 os.remove(temp_file) |
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143 |
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144 if errors: |
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145 print("%i sequences, %i positive, %i errors" |
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146 % (count, positive, errors)) |
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147 else: |
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148 print("%i/%i sequences positive" % (positive, count)) |
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149 |
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150 if count and count==errors: |
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151 # Galaxy will still allow them to see the output file |
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152 stop_err("All your sequences gave an error code") |