Mercurial > repos > peterjc > effectivet3
annotate tools/effectiveT3/effectiveT3.py @ 11:392279f2e120 draft
Uploaded v0.0.12, more explicit output name
| author | peterjc |
|---|---|
| date | Thu, 23 May 2013 13:11:09 -0400 |
| parents | b863c4bec840 |
| children | 17fbf8b8a554 |
| rev | line source |
|---|---|
| 2 | 1 #!/usr/bin/env python |
| 2 """Wrapper for EffectiveT3 v1.0.1 for use in Galaxy. | |
| 3 | |
| 4 This script takes exactly five command line arguments: | |
| 5 * model name (e.g. TTSS_STD-1.0.1.jar) | |
| 6 * threshold (selective or sensitive) | |
| 7 * an input protein FASTA filename | |
| 8 * output tabular filename | |
| 9 | |
| 10 It then calls the standalone Effective T3 v1.0.1 program (not the | |
| 11 webservice), and reformats the semi-colon separated output into | |
| 12 tab separated output for use in Galaxy. | |
| 13 """ | |
| 14 import sys | |
| 15 import os | |
| 16 import subprocess | |
| 17 | |
| 18 #The Galaxy auto-install via tool_dependencies.xml will set this environment variable | |
| 19 effectiveT3_dir = os.environ.get("EFFECTIVET3", "/opt/EffectiveT3/") | |
| 20 effectiveT3_jar = os.path.join(effectiveT3_dir, "TTSS_GUI-1.0.1.jar") | |
| 21 | |
| 22 if "-v" in sys.argv or "--version" in sys.argv: | |
| 23 #TODO - Get version of the JAR file dynamically? | |
| 24 print "Wrapper v0.0.11, TTSS_GUI-1.0.1.jar" | |
| 25 sys.exit(0) | |
| 26 | |
| 27 def stop_err(msg, error_level=1): | |
| 28 """Print error message to stdout and quit with given error level.""" | |
| 29 sys.stderr.write("%s\n" % msg) | |
| 30 sys.exit(error_level) | |
| 31 | |
| 32 if len(sys.argv) != 5: | |
| 33 stop_err("Require four arguments: model, threshold, input protein FASTA file & output tabular file") | |
| 34 | |
| 35 model, threshold, fasta_file, tabular_file = sys.argv[1:] | |
| 36 | |
| 37 if not os.path.isfile(fasta_file): | |
| 38 stop_err("Input FASTA file not found: %s" % fasta_file) | |
| 39 | |
| 40 if threshold not in ["selective", "sensitive"] \ | |
| 41 and not threshold.startswith("cutoff="): | |
| 42 stop_err("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold) | |
| 43 | |
| 44 def clean_tabular(raw_handle, out_handle): | |
| 45 """Clean up Effective T3 output to make it tabular.""" | |
| 46 count = 0 | |
| 47 positive = 0 | |
| 48 errors = 0 | |
| 49 for line in raw_handle: | |
| 50 if not line or line.startswith("#") \ | |
| 51 or line.startswith("Id; Description; Score;"): | |
| 52 continue | |
| 53 assert line.count(";") >= 3, repr(line) | |
| 54 #Normally there will just be three semi-colons, however the | |
| 55 #original FASTA file's ID or description might have had | |
| 56 #semi-colons in it as well, hence the following hackery: | |
| 57 try: | |
| 58 id_descr, score, effective = line.rstrip("\r\n").rsplit(";",2) | |
| 59 #Cope when there was no FASTA description | |
| 60 if "; " not in id_descr and id_descr.endswith(";"): | |
| 61 id = id_descr[:-1] | |
| 62 descr = "" | |
| 63 else: | |
| 64 id, descr = id_descr.split("; ",1) | |
| 65 except ValueError: | |
| 66 stop_err("Problem parsing line:\n%s\n" % line) | |
| 67 parts = [s.strip() for s in [id, descr, score, effective]] | |
| 68 out_handle.write("\t".join(parts) + "\n") | |
| 69 count += 1 | |
| 70 if float(score) < 0: | |
| 71 errors += 1 | |
| 72 if effective.lower() == "true": | |
| 73 positive += 1 | |
| 74 return count, positive, errors | |
| 75 | |
| 76 def run(cmd): | |
| 77 #Avoid using shell=True when we call subprocess to ensure if the Python | |
| 78 #script is killed, so too is the child process. | |
| 79 try: | |
| 80 child = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE) | |
| 81 except Exception, err: | |
| 82 stop_err("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err)) | |
| 83 #Use .communicate as can get deadlocks with .wait(), | |
| 84 stdout, stderr = child.communicate() | |
| 85 return_code = child.returncode | |
| 86 if return_code: | |
| 87 if stderr and stdout: | |
| 88 stop_err("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, err, stdout, stderr)) | |
| 89 else: | |
| 90 stop_err("Return code %i from command:\n%s\n%s" % (return_code, err, stderr)) | |
| 91 | |
| 92 if not os.path.isdir(effectiveT3_dir): | |
|
8
4a0aa59062f7
Uploaded v0.0.11, take 9, debug output if can't find model
peterjc
parents:
2
diff
changeset
|
93 stop_err("Effective T3 folder not found: %r" % effectiveT3_dir) |
| 2 | 94 |
| 95 if not os.path.isfile(effectiveT3_jar): | |
|
8
4a0aa59062f7
Uploaded v0.0.11, take 9, debug output if can't find model
peterjc
parents:
2
diff
changeset
|
96 stop_err("Effective T3 JAR file not found: %r" % effectiveT3_jar) |
| 2 | 97 |
|
9
b863c4bec840
Uploaded v0.0.11, take 10, debug output if module folder missing
peterjc
parents:
8
diff
changeset
|
98 if not os.path.isdir(os.path.join(effectiveT3_dir, "module")): |
|
b863c4bec840
Uploaded v0.0.11, take 10, debug output if module folder missing
peterjc
parents:
8
diff
changeset
|
99 stop_err("Effective T3 module folder not found: %r" % os.path.join(effectiveT3_dir, "module")) |
|
b863c4bec840
Uploaded v0.0.11, take 10, debug output if module folder missing
peterjc
parents:
8
diff
changeset
|
100 |
| 2 | 101 effectiveT3_model = os.path.join(effectiveT3_dir, "module", model) |
| 102 if not os.path.isfile(effectiveT3_model): | |
|
8
4a0aa59062f7
Uploaded v0.0.11, take 9, debug output if can't find model
peterjc
parents:
2
diff
changeset
|
103 sys.stderr.write("Contents of %r is %s\n" |
|
4a0aa59062f7
Uploaded v0.0.11, take 9, debug output if can't find model
peterjc
parents:
2
diff
changeset
|
104 % (os.path.join(effectiveT3_dir, "module"), |
|
4a0aa59062f7
Uploaded v0.0.11, take 9, debug output if can't find model
peterjc
parents:
2
diff
changeset
|
105 ", ".join(repr(p) for p in os.listdir(os.path.join(effectiveT3_dir, "module"))))) |
|
4a0aa59062f7
Uploaded v0.0.11, take 9, debug output if can't find model
peterjc
parents:
2
diff
changeset
|
106 sys.stderr.write("Main JAR was found: %r\n" % effectiveT3_jar) |
|
4a0aa59062f7
Uploaded v0.0.11, take 9, debug output if can't find model
peterjc
parents:
2
diff
changeset
|
107 stop_err("Effective T3 model JAR file not found: %r" % effectiveT3_model) |
| 2 | 108 |
| 109 #We will have write access whereever the output should be, | |
| 110 temp_file = os.path.abspath(tabular_file + ".tmp") | |
| 111 | |
| 112 #Use absolute paths since will change current directory... | |
| 113 tabular_file = os.path.abspath(tabular_file) | |
| 114 fasta_file = os.path.abspath(fasta_file) | |
| 115 | |
| 116 cmd = ["java", "-jar", effectiveT3_jar, | |
| 117 "-f", fasta_file, | |
| 118 "-m", model, | |
| 119 "-t", threshold, | |
| 120 "-o", temp_file, | |
| 121 "-q"] | |
| 122 | |
| 123 try: | |
| 124 #Must run from directory above the module subfolder: | |
| 125 os.chdir(effectiveT3_dir) | |
| 126 except: | |
| 127 stop_err("Could not change to Effective T3 folder: %s" % effectiveT3_dir) | |
| 128 | |
| 129 run(cmd) | |
| 130 | |
| 131 if not os.path.isfile(temp_file): | |
| 132 stop_err("ERROR - No output file from Effective T3") | |
| 133 | |
| 134 out_handle = open(tabular_file, "w") | |
| 135 out_handle.write("#ID\tDescription\tScore\tEffective\n") | |
| 136 data_handle = open(temp_file) | |
| 137 count, positive, errors = clean_tabular(data_handle, out_handle) | |
| 138 data_handle.close() | |
| 139 out_handle.close() | |
| 140 | |
| 141 os.remove(temp_file) | |
| 142 | |
| 143 if errors: | |
| 144 print "%i sequences, %i positive, %i errors" \ | |
| 145 % (count, positive, errors) | |
| 146 else: | |
| 147 print "%i/%i sequences positive" % (positive, count) | |
| 148 | |
| 149 if count and count==errors: | |
| 150 #Galaxy will still allow them to see the output file | |
| 151 stop_err("All your sequences gave an error code") |