Mercurial > repos > blankenberg > column_regex_substitution

annotate column_regex_substitution.py @ 0:12b740c4cbc1 draft default tip

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planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
author blankenberg
date Fri, 07 Sep 2018 10:29:30 -0400
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0
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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1 #!/usr/bin/env python
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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2 #Dan Blankenberg
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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3
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4 """
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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5 A script for using regex substitutions on columns.
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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6 """
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7
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8 import optparse
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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9 import re
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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10 import sys
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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11 import string
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12
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13 VERSION = "0.0.1"
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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15 COLUMN_STRIP_VALUES = "".join( set( string.printable ) - set( string.digits ) - set(',') )
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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17 def get_provided_columns( provided_value, column_offset ):
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18 try:
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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19 rval = sorted( map( lambda x: int( x.strip( COLUMN_STRIP_VALUES ) ) + column_offset, provided_value.split( ',' ) ) )
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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20 except:
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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21 rval = None
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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22 if rval:
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23 return rval
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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24 return None
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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27 def __main__():
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28 parser = optparse.OptionParser()
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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29 parser.add_option('--pattern', action='store', default=None,
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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30 help='pattern string')
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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31 parser.add_option('--replacement', action='store', default=None,
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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32 help='replacement string')
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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33 parser.add_option('--input', action='store', default=None,
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
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34 help='Filename of input file')
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35 parser.add_option('--output', action='store', default=None,
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36 help='Filename of output file')
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37 parser.add_option('--delimiter', action='store', default=None,
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38 help='column delimiter')
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39 parser.add_option('--columns', action='store', default=None,
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40 help='columns to operate on')
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41 parser.add_option('--column_offset', action='store', default=0,
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42 help='offset to apply to columns index to force to zero-based')
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43 parser.add_option('--skip', action='store', default=0,
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44 help='Number of lines to skip')
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45 parser.add_option('--version', action='store_true', default=False,
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46 help='Show version')
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47
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48 (options, args) = parser.parse_args()
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49
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50 if options.version:
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51 print "blankenberg_python_regex_substitution %s" % ( VERSION )
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52 sys.exit(0)
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53
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54 if None in [ options.pattern, options.replacement, options.output ]:
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55 parser.print_help()
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56 sys.exit(1)
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57
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58 pattern = options.pattern
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59 replacement = options.replacement
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60 column_offset = int( options.column_offset )
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61 print "Pattern: %s\nReplacement: %s" % ( repr( pattern ), repr( replacement ) )
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62 pattern = re.compile( pattern )
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63 provided_columns = get_provided_columns( options.columns, column_offset )
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64 if provided_columns:
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65 column_str = ", ".join( map( lambda x: str( x - column_offset ), provided_columns ) )
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66 else:
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67 column_str = 'all'
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68 print "With delimiter %s, on columns: %s" % ( repr( options.delimiter ), column_str )
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69 if options.delimiter is None:
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70 split_func = lambda x: [ x.rstrip( '\n\r' ) ]
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71 join_char = ""
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72 else:
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73 split_func = lambda x: x.rstrip( '\n\r' ).split( options.delimiter )
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74 join_char = options.delimiter
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75 with open( options.input, 'rb' ) as fin:
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76 with open( options.output, 'w') as fout:
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77 for i, line in enumerate( fin ):
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78 if i < options.skip:
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79 continue
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80 line = split_func( line )
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81 field_count = len( line )
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82 if provided_columns:
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83 columns = provided_columns
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84 else:
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85 columns = range( field_count )
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86 for j in columns:
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87 if j >= field_count:
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
blankenberg
parents:
diff changeset
88 break
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
blankenberg
parents:
diff changeset
89 line[ j ] = re.sub( pattern, replacement, line[ j ] )
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
blankenberg
parents:
diff changeset
90 fout.write( "%s\n" % ( join_char.join( line ) ) )
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
blankenberg
parents:
diff changeset
91
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
blankenberg
parents:
diff changeset
92 if __name__ == "__main__":
12b740c4cbc1 planemo upload for repository https://github.com/blankenberg/tools-blankenberg/tree/master/tools/column_regex_substitution commit 78936dc6be1747303d4cbfd80d09e4cfd1cbf292
blankenberg
parents:
diff changeset
93 __main__()