### Navigation

- index
- modules |
- SamSifter 0.5.0 documentation »
- Module code »

# Source code for samsifter.util.filters

    #!/usr/bin/env python3
    # -*- coding: utf-8 -*-
    """Basic filtering operations on files.

    .. moduleauthor:: Florian Aldehoff <faldehoff@student.uni-tuebingen.de>
    """
    import re
    import sys
    import fileinput

    def pattern_filter(patterns, filehandle, discard=True):
        """Emulates grep-like inverse pattern search.

        Emulates the behaviour of ``grep -v -f PATTERNFILE`` and prints only
        non-matching lines to STDOUT. Inverse operation to print only lines
        matching at least one of the patterns by setting discard to False.

        Parameters
        ----------
        patterns : list of str
            List of string patterns to search.
        filehandle : File
            Opened and readable file object.
        discard : bool, optional
            Print only lines matching none of the patterns to STDOUT. Defaults to
            True.

        Returns
        -------
        bool
            True on successful filtering, False on empty pattern list or other
            error.
        """
        if len(patterns) == 0:
            return False

        # create long search string of patterns separated by | (OR)
        # escape '|' in individual patterns, eg. for taxa and references
        searchstring = re.escape(patterns[0])
        for pattern in patterns[1:]:
            searchstring += "|" + re.escape(pattern)

    #    print("search string: %s\n" % searchstring, file=sys.stderr)

        for line in filehandle:
            if line.startswith('@'):
                print(line.rstrip(), file=sys.stdout)
            else:
                result = re.search(searchstring, line)
                if result:
                    if not discard:
                        print(line.rstrip(), file=sys.stdout)
                else:
                    if discard:
                        print(line.rstrip(), file=sys.stdout)
        return True

    def line_filter(lines, filehandle, discard=True, offset=0):
        """Filters specific lines from a file.

        Prints only lines not contained in list to STDOUT while ignoring the number
        of lines in the beginning as defined by offset (default is 0 = no header).
        Inverse operation to print only lines contained in list by setting
        ``discard`` to False.

        Parameters
        ----------
        lines : list of int
            List of line numbers to remove from file. Line numbers are considered
            to be 0-based unless an offset is specified. List can be unsorted and
            duplicates will be removed prior to filtering.
        filehandle : File
            Opened and readable file object.
        discard : bool, optional
            Print only lines matching none of the entries to STDOUT. Defaults to
            True.
        offset: int, optional
            Positive offset for line numbers to be used in case the
            cursor of the filehandle has placed after the start of the line
            numbering ('fast forward'). Useful to skip header sections of a file.

        Returns
        -------
        bool
            True on success, False on empty list.

        Raises
        ------
        Exception
            If file ends before all specified lines are filtered (indicating wrong
            use of the offset parameter).
        IndexError
            If first line to be filtered is within the specified offset.
        ValueError
            If offset is negative.
        """
        if len(lines) == 0:
            return False

        if offset < 0:
            raise ValueError("negative filtering offset %i not supported" % offset)

        # sort lines to be filtered and remove duplicate entries
        lines = sorted(list(set(lines)), reverse=True)
        next_line = lines.pop()

        # prevent filtering of negative indices (first line to be filtered is
        # within offset)
        if next_line <= offset:
            raise IndexError("first filtered line %i <= offset %i"
                             % (next_line, offset))

        for num, line in enumerate(filehandle):
            if (next_line is not None) and (num == next_line - offset):
                if not discard:
                    print(line.rstrip(), file=sys.stdout)
                try:
                    next_line = lines.pop()
                except IndexError:
                    next_line = None
            else:
                if discard:
                    print(line.rstrip(), file=sys.stdout)

        # warn if there are still lines left to be filtered
        if next_line is not None:
            raise Exception("%i unfiltered line(s)" % (len(lines) + 1))

        return True

    def main(argv):
        """Simple test of pattern_filter and line_filter methods."""
        handle = fileinput.input()
    #    textfile = '/home/aldehoff/sandbox/alice.txt'
    #    handle = open(textfile, mode='r')

    #    patterns = ["lexicon", "fox", "Rabbit"]
    #    pattern_filter(patterns, handle, False)

        lines = [2, 3, 4, 20, 44, 34]
        # Result should include desired line numbers in correct order. If offset
        # is given the appropriate numbers of lines should be skipped.
        print(line_filter(lines, handle, False, offset=0), file=sys.stderr)

    if __name__ == '__main__':
        main(sys.argv)

### Navigation

- index
- modules |
- SamSifter 0.5.0 documentation »
- Module code »