tanghaibao /
goatools
| @@ 68-84 (lines=17) @@ | ||
| 65 | prt.write(" {N} GO IDs READ: {TXT}\n".format(N=len(goids), TXT=go_file)) |
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| 66 | return goids |
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| 67 | ||
| 68 | @staticmethod |
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| 69 | def get_goargs(go_args, prt): |
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| 70 | """Get GO IDs and colors for GO IDs from the GO ID runtime arguments.""" |
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| 71 | goids = set() |
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| 72 | go2color = {} |
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| 73 | # Match on "GO ID" or "GO ID and color" |
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| 74 | re_gocolor = re.compile(r'(GO:\d{7})((?:#[0-9a-fA-F]{6})?)') |
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| 75 | for go_arg in go_args: |
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| 76 | mtch = re_gocolor.match(go_arg) |
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| 77 | if mtch: |
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| 78 | goid, color = mtch.groups() |
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| 79 | goids.add(goid) |
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| 80 | if color: |
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| 81 | go2color[goid] = color |
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| 82 | elif prt: |
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| 83 | prt.write("WARNING: UNRECOGNIZED ARG({})".format(go_arg)) |
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| 84 | return goids |
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| 85 | ||
| 86 | # Copyright (C) 2016-2018, DV Klopfenstein, H Tang. All rights reserved. |
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| 87 | ||
| @@ 122-137 (lines=16) @@ | ||
| 119 | return [ret['GOs'], ret['go2color']] |
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| 120 | ||
| 121 | def _goargs(self, ret, go_args): |
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| 122 | """Get GO IDs and colors for GO IDs from the GO ID runtime arguments.""" |
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| 123 | goids = set() |
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| 124 | go2color = {} |
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| 125 | # Match on "GO ID" or "GO ID and color" |
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| 126 | re_gocolor = re.compile(r'(GO:\d{7})((?:#[0-9a-fA-F]{6})?)') |
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| 127 | for go_arg in go_args: |
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| 128 | mtch = re_gocolor.match(go_arg) |
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| 129 | if mtch: |
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| 130 | goid, color = mtch.groups() |
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| 131 | goids.add(goid) |
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| 132 | if color: |
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| 133 | go2color[goid] = color |
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| 134 | else: |
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| 135 | print("WARNING: UNRECOGNIZED ARG({})".format(go_arg)) |
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| 136 | self._update_ret(ret, goids, go2color) |
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| 137 | ||
| 138 | def _rdtxt_gos(self, ret, go_file): |
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| 139 | """Read GO IDs from a file.""" |
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| 140 | if not os.path.exists(go_file): |
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