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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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