Mercurial > repos > peterjc > effectivet3
annotate tools/effectiveT3/effectiveT3.py @ 32:1129cafdf0ae draft
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
author | peterjc |
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date | Wed, 07 Jun 2017 10:51:31 -0400 |
parents | 3ef6c246ccac |
children | 011cfce866f1 |
rev | line source |
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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 os | |
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1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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15 # We want to be able to use shutil.which, but need Python 3.3+ |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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16 # import shutil |
2 | 17 import subprocess |
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69ba0f4e91af
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 5fb6ee31f33e8e24c1ae5d56c93ac3e0157dad72-dirty
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18 import sys |
2 | 19 |
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1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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20 # The Galaxy auto-install via tool_dependencies.xml will set the |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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21 # environment variable $EFFECTIVET3 pointing at the folder with |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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22 # the JAR file. |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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23 # |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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24 # The BioConda recipe will put a wrapper script on the $PATH, |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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25 # which we can use to find the JAR file. |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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26 # |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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27 # We fall back on /opt/EffectiveT3/ |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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28 # |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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29 effective_t3_jarname = "TTSS_GUI-1.0.1.jar" |
2 | 30 |
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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1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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33 print("Wrapper v0.0.20, for %s" % effective_t3_jarname) |
2 | 34 sys.exit(0) |
35 | |
36 if len(sys.argv) != 5: | |
23 | 37 sys.exit("Require four arguments: model, threshold, input protein FASTA file & output tabular file") |
2 | 38 |
39 model, threshold, fasta_file, tabular_file = sys.argv[1:] | |
40 | |
41 if not os.path.isfile(fasta_file): | |
23 | 42 sys.exit("Input FASTA file not found: %s" % fasta_file) |
2 | 43 |
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a3d660e900b1
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 7a746d55f0e8456992ee11c49a507285f9f39383-dirty
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44 if threshold not in ["selective", "sensitive"] and not threshold.startswith("cutoff="): |
23 | 45 sys.exit("Threshold should be selective, sensitive, or cutoff=..., not %r" % threshold) |
46 | |
2 | 47 |
48 def clean_tabular(raw_handle, out_handle): | |
49 """Clean up Effective T3 output to make it tabular.""" | |
50 count = 0 | |
51 positive = 0 | |
52 errors = 0 | |
53 for line in raw_handle: | |
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a3d660e900b1
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 7a746d55f0e8456992ee11c49a507285f9f39383-dirty
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54 if not line or line.startswith("#") or line.startswith("Id; Description; Score;"): |
2 | 55 continue |
56 assert line.count(";") >= 3, repr(line) | |
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57 # Normally there will just be three semi-colons, however the |
17fbf8b8a554
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58 # original FASTA file's ID or description might have had |
17fbf8b8a554
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59 # semi-colons in it as well, hence the following hackery: |
2 | 60 try: |
23 | 61 id_descr, score, effective = line.rstrip("\r\n").rsplit(";", 2) |
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17fbf8b8a554
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62 # Cope when there was no FASTA description |
2 | 63 if "; " not in id_descr and id_descr.endswith(";"): |
64 id = id_descr[:-1] | |
65 descr = "" | |
66 else: | |
23 | 67 id, descr = id_descr.split("; ", 1) |
2 | 68 except ValueError: |
23 | 69 sys.exit("Problem parsing line:\n%s\n" % line) |
2 | 70 parts = [s.strip() for s in [id, descr, score, effective]] |
71 out_handle.write("\t".join(parts) + "\n") | |
72 count += 1 | |
73 if float(score) < 0: | |
23 | 74 errors += 1 |
2 | 75 if effective.lower() == "true": |
23 | 76 positive += 1 |
2 | 77 return count, positive, errors |
78 | |
23 | 79 |
2 | 80 def run(cmd): |
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af14f755c05b
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 7496128ee9ef800fe780e545d2157da8a4f89d35-dirty
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81 """Run the command line string via subprocess.""" |
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17fbf8b8a554
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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. |
2 | 84 try: |
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3ef6c246ccac
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 79bbb921cb5aa953f0323accd6c8c293c6e486cf-dirty
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85 child = subprocess.Popen(cmd, universal_newlines=True, |
3ef6c246ccac
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 79bbb921cb5aa953f0323accd6c8c293c6e486cf-dirty
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86 stdout=subprocess.PIPE, stderr=subprocess.PIPE) |
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35c358aa7801
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit 37d5b47ec23e2cbaa453cc660bb1fcbb10dd34ee-dirty
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87 except Exception as err: |
23 | 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(), |
2 | 90 stdout, stderr = child.communicate() |
91 return_code = child.returncode | |
18 | 92 if return_code or stderr.startswith("Exception in thread"): |
23 | 93 cmd_str = " ".join(cmd) # doesn't quote spaces etc |
2 | 94 if stderr and stdout: |
23 | 95 sys.exit("Return code %i from command:\n%s\n\n%s\n\n%s" % (return_code, cmd_str, stdout, stderr)) |
2 | 96 else: |
23 | 97 sys.exit("Return code %i from command:\n%s\n%s" % (return_code, cmd_str, stderr)) |
2 | 98 |
18 | 99 |
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1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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100 try: |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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101 from shutil import which |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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102 except ImportError: |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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103 # Likely running on Python 2, use backport: |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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104 def which(cmd, mode=os.F_OK | os.X_OK, path=None): |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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105 """Given a command, mode, and a PATH string, return the path which |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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106 conforms to the given mode on the PATH, or None if there is no such |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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107 file. |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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108 `mode` defaults to os.F_OK | os.X_OK. `path` defaults to the result |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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112 |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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113 # Check that a given file can be accessed with the correct mode. |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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116 def _access_check(fn, mode): |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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126 |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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127 if sys.platform == "win32": |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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130 path.insert(0, os.curdir) |
2 | 131 |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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) |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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134 # See if the given file matches any of the expected path extensions. |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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135 # This will allow us to short circuit when given "python.exe". |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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136 matches = [cmd for ext in pathext if cmd.lower().endswith(ext.lower())] |
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planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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] |
1129cafdf0ae
planemo upload for repository https://github.com/peterjc/pico_galaxy/tree/master/tools/effectiveT3 commit b557cc18c85dcc5147b80c71f99c16a7015e12b2-dirty
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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)) |
2 | 179 |
23 | 180 if not os.path.isdir(os.path.join(effective_t3_dir, "module")): |
181 sys.exit("Effective T3 module folder not found: %r" % os.path.join(effective_t3_dir, "module")) | |
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182 |
23 | 183 effective_t3_model = os.path.join(effective_t3_dir, "module", model) |
184 if not os.path.isfile(effective_t3_model): | |
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185 sys.stderr.write("Contents of %r is %s\n" |
23 | 186 % (os.path.join(effective_t3_dir, "module"), |
187 ", ".join(repr(p) for p in os.listdir(os.path.join(effective_t3_dir, "module"))))) | |
188 sys.stderr.write("Main JAR was found: %r\n" % effective_t3_jar) | |
189 sys.exit("Effective T3 model JAR file not found: %r" % effective_t3_model) | |
2 | 190 |
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191 # We will have write access wherever the output should be, |
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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") |
2 | 196 |
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197 # Use absolute paths since will change current directory... |
2 | 198 tabular_file = os.path.abspath(tabular_file) |
199 fasta_file = os.path.abspath(fasta_file) | |
200 | |
23 | 201 cmd = ["java", "-jar", effective_t3_jar, |
2 | 202 "-f", fasta_file, |
203 "-m", model, | |
204 "-t", threshold, | |
205 "-o", temp_file, | |
206 "-q"] | |
207 | |
208 try: | |
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209 # Must run from directory above the module subfolder: |
23 | 210 os.chdir(effective_t3_dir) |
211 except Exception: | |
212 sys.exit("Could not change to Effective T3 folder: %s" % effective_t3_dir) | |
2 | 213 |
214 run(cmd) | |
215 | |
216 if not os.path.isfile(temp_file): | |
23 | 217 sys.exit("ERROR - No output file from Effective T3") |
2 | 218 |
219 out_handle = open(tabular_file, "w") | |
220 out_handle.write("#ID\tDescription\tScore\tEffective\n") | |
221 data_handle = open(temp_file) | |
222 count, positive, errors = clean_tabular(data_handle, out_handle) | |
223 data_handle.close() | |
224 out_handle.close() | |
225 | |
226 os.remove(temp_file) | |
227 | |
228 if errors: | |
23 | 229 print("%i sequences, %i positive, %i errors" |
230 % (count, positive, errors)) | |
2 | 231 else: |
23 | 232 print("%i/%i sequences positive" % (positive, count)) |
2 | 233 |
23 | 234 if count and count == errors: |
235 # Galaxy will still allow them to see the output file | |
236 sys.exit("All your sequences gave an error code") |