sharplabtool: tools/validation/fix

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+:9071e359b9a3
+#!/usr/bin/env python
+"""
+Fix errors in a dataset.
+For now, only removing erroneous lines is supported.
+usage: %prog input errorsfile output
+-x, --ext: dataset extension (type)
+-m, --methods=N: comma separated list of repair methods
+"""
+import pkg_resources; pkg_resources.require( "bx-python" )
+from bx.cookbook import doc_optparse
+from galaxy import util
+def main():
+options, args = doc_optparse.parse( __doc__ )
+methods = []
+try:
+if options.methods: methods = options.methods.split(",")
+except:
+pass
+ext = options.ext
+in_file = open(args[0], "r")
+error_file = open(args[1], "r")
+out_file = open(args[2], "w")
+# string_to_object errors
+error_list = util.string_to_object(error_file.read())
+# index by error type and then by line number
+error_lines = {}
+error_types = {}
+for error in error_list:
+if error.linenum:
+if error.linenum in error_lines:
+error_lines[error.linenum].append(error)
+else:
+error_lines[error.linenum] = [error]
+error_type = error.__class__.__name__
+if error_type in error_types:
+error_types[error_type].append(error)
+else:
+error_types[error_type] = [error]
+linenum = 0
+for line in in_file:
+linenum += 1
+# write unless
+if "lines" in methods:
+if linenum in error_lines:
+line = None
+# other processing here?
+if line:
+out_file.write(line)
+if __name__ == "__main__":
+main()

Mercurial > repos > xuebing > sharplabtool