Package Bio :: Module FilteredReader
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Module FilteredReader

source code

Code for more fancy file handles (OBSOLETE).

Classes: Filtered is a decorator for File that allows the user to filter the output on a line by line basis.

The FilteredReader module reads a file and applies a sequence of filters to the input The constructor sets a default filter chain, but the user can select another filter by setting Bio.FilteredReader.filter_chain.

handle = open( "filename" ) filtered_reader = Bio.FilteredReader( handle ) filtered_reader.filter_chain = [ remove_asterisks, replace_dot_with_dash ] filtered_reasder.read()

All filters in the chain must provide the same interface with a line of text as the single input parameter and altered text as the return value.

This module is now considered to be obsolete, and is likely to be deprecated in a future release of Biopython, and later removed.

Classes [hide private]
  FilteredReader
Functions [hide private]
 
dump_saved(name, text, j)
Used for debugging.
source code
 
remove_leading_whitespace(line) source code
 
remove_empty_line(line) source code
 
remove_useless_dot(line) source code
 
fix_punctuation(line) source code
 
has_trailing_linefeed(line) source code