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FilteredReader.py

# Copyright 2001 by Katharine Lindner.  All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license.  Please see the LICENSE file that should have been included
# as part of this package.

"""Code for more fancy file handles.

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.

"""

import os
import string
import copy
from File import UndoHandle



"""Used for debugging"""
def dump_saved( name, text, j ):
    dump_file = open( name + '%d' % j, "w" )
    k = 0
    for i in range ( 0, len( text ), 80 ):
        dump_file.write(  '%s\n' % text[ i : i + 80 ] )
    dump_file.close()

def remove_leading_whitespace( line ):
    return line.lstrip()


def remove_empty_line( line ):
    stripped_line = line.strip()
    if( stripped_line ):
        return line[ : ]
    else:
        return ''

def remove_useless_dot( line ):
    before = line
    while( 1 ):
        after = before.replace( "\t.\t", "\t\t" )
        if( len( before ) == len( after ) ):
            break
        before = after
    if( after.endswith( '.' ) ):
        after = after[ :-1 ]
    return after

def fix_punctuation( line ):
    line = line.replace( "'", '' )
    line = line.replace( '"', '' )
    line = line.replace( ';', '\t' )
    line = line.replace( 'entryname', 'id' )
#    line = line.lower( )
    if( line ):
        return line[ : ]
    else:
        return ''



class FilteredReader:
    def __init__(self, handle ):
        self._handle = handle
        self._start_line = ''
        self._debug_count = 0
        self.filter_chain = [ remove_empty_line, remove_useless_dot, fix_punctuation ]

    def __getattr__(self, attr):
        return getattr(self._handle, attr)



    def close(self, *args, **keywds ):
        return self._handle.close( *args, **keywds)

    def read( self, *args, **keywds ):
        line = ''
        len_expected = self._get_len_expected( args, keywds )
        if( len_expected ):
            filtered_text = self.read_block( len_expected )
        else:
            filtered_text = self.read_to_end()
        return filtered_text

    def read_block( self, len_expected ):

        len_filtered = 0
        len_adjusted = len_expected - len( self._start_line )
        filtered_text = ''
        while( len_filtered < len_expected ):

            text_read = self._handle.read( len_adjusted )
            full_text = self._start_line + text_read
            lines = full_text.splitlines( 1 )
            if( text_read == '' ):
                filtered_text = filtered_text + self.filter( lines )
                break
            else:
                all_but_last_line = lines[ :-1 ]
                self._start_line = lines[ -1 ]
                filtered_text = filtered_text + self.filter( all_but_last_line )
            len_filtered_text = len( filtered_text )
            len_adjusted = len_adjusted - len_filtered_text
        return filtered_text[ : ]

    def read_to_end( self ):
        filtered_text = ''
        text_read = self._handle.read()
        full_text = self._start_line + text_read
        lines = full_text.splitlines( 1 )
        filtered_text = filtered_text + self.filter( lines[:] )
        return filtered_text[ : ]






    def _get_len_expected( self, args, keywds ):

        if( len( args) > 0 ):
            len_expected = args[ 0 ]
            if( len_expected < 0 ):
                len_expected = None
        elif( keywds.has_key( 'size' ) ):
            len_expected = keywds[ 'size' ]
        else:
            len_expected = None
        return len_expected

    def filter( self, lines  ):
        filter_chain = self.filter_chain
        filtered_text = ''
        for line in lines:
            for filter in filter_chain:
                line = filter( *( line, ) )
            filtered_text = filtered_text + line

        return filtered_text

def has_trailing_linefeed( line ):
    if( line.endswith( chr( 13 ) ) or \
        line.endswith( chr( 10 ) ) ):
        return 1
    else:
        return 0

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