[2] | 1 | #!/usr/bin/env python |
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| 2 | |
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| 3 | """ |
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| 4 | Fix errors in a dataset. |
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| 5 | For now, only removing erroneous lines is supported. |
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| 6 | |
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| 7 | usage: %prog input errorsfile output |
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| 8 | -x, --ext: dataset extension (type) |
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| 9 | -m, --methods=N: comma separated list of repair methods |
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| 10 | """ |
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| 11 | |
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| 12 | import pkg_resources; pkg_resources.require( "bx-python" ) |
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| 13 | from bx.cookbook import doc_optparse |
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| 14 | |
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| 15 | from galaxy import util |
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| 16 | |
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| 17 | def main(): |
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| 18 | options, args = doc_optparse.parse( __doc__ ) |
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| 19 | methods = [] |
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| 20 | try: |
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| 21 | if options.methods: methods = options.methods.split(",") |
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| 22 | except: |
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| 23 | pass |
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| 24 | |
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| 25 | ext = options.ext |
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| 26 | |
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| 27 | in_file = open(args[0], "r") |
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| 28 | error_file = open(args[1], "r") |
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| 29 | out_file = open(args[2], "w") |
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| 30 | |
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| 31 | # string_to_object errors |
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| 32 | error_list = util.string_to_object(error_file.read()) |
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| 33 | # index by error type and then by line number |
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| 34 | error_lines = {} |
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| 35 | error_types = {} |
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| 36 | for error in error_list: |
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| 37 | if error.linenum: |
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| 38 | if error.linenum in error_lines: |
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| 39 | error_lines[error.linenum].append(error) |
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| 40 | else: |
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| 41 | error_lines[error.linenum] = [error] |
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| 42 | error_type = error.__class__.__name__ |
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| 43 | if error_type in error_types: |
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| 44 | error_types[error_type].append(error) |
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| 45 | else: |
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| 46 | error_types[error_type] = [error] |
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| 47 | |
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| 48 | linenum = 0 |
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| 49 | for line in in_file: |
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| 50 | linenum += 1 |
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| 51 | # write unless |
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| 52 | if "lines" in methods: |
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| 53 | if linenum in error_lines: |
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| 54 | line = None |
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| 55 | # other processing here? |
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| 56 | if line: |
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| 57 | out_file.write(line) |
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| 58 | |
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| 59 | if __name__ == "__main__": |
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| 60 | main() |
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