FFM(1)                        FERRET UTILITY                      FFM(1)

NAME
    ffm - Ferret Filename Manager

SYNOPSIS
    ffm [-l] [-t threshold]

DESCRIPTION
    This program allows the user to interactively modify ferret(1)'s
    file containing filename post-processing rules (henceforth called
    the "rulefile") and to apply the new rules to the filenames
    of the sequences in the FERRETBANK directory.

    On invocation, the program reads all the sequence filenames in the
    FERRETBANK directory and the content of the FERRET.RULES (also
    located in this directory). The sequence filenames are assumed to
    be those containing at least one "-". A list of all the words
    with frequency count greater than or equeal to threshold (by default,
    10) found in the filenames is then shown.

    Here is a brief description of the three options of the main menu.

    1- Edit rules file:
        A copy of the rules file is saved in a temporary file, and
        the editor specified in the environment variable EDITOR is
        summoned on this temporary file. The new content replaces
        the internal copy of the file kept in memory. It does NOT
        replaces the rulefile in the FERRETBANK directory.
    2- Test rule file:
        For each sequence filename read in the FERRETBANK directory,
        the rules in the rulefile (from the ruleset "FILENAMES") are
        applied. If a filename change following the application of those
        rules, the use is asked whether the modification is to be retained
        or not. When all filenames have been processed and at least one
        change confirmed, the user is asked whether the filenames in
        FERRETBANK should be renamed. If the user says so, renaming occurs,
        and the INDEX file in the FERRETBANK directory is updated too if
        it is present.
    3- Save rule file:
        The current internal copy of the rule file is saved back in the
        FERRETBANK directory.

OPTIONS
    -l Use FERRETBANK=cwd rather than the hardcoded path found in the
       ferret.conf file.

    -t Set the threshold for reporting word frequency.

ENVIRONMENT
    EDITOR                   - The user's favorite text editor
    USER                     - Necessary to create the user's temporary files.

FILES
    $PERLLIB/ogmp/ferret.conf  - A configuration file containing many
                                 absolute paths definitions. $PERLLIB is
                                 the standard perl library path.
    $FERRETBANK                - Set in ferret.conf, overridden by -l option.
                                 Sequence files are found (and renamed) there.
    $FERRETBANK/Report/        - Reports are found (and renamed) there.
    $FERRETBANK/Support/INDEX  - Ferret INDEX file.
    $FERRETBANK/Support/ffmlog - Where some serious error message may appear.
    $FERRETBANK/Support/FERRET.RULES - The rulefile.
    /tmp/tmp.ffm.$USER.$$      - Temp file used when editing the rule file.

SEE ALSO
    rulepack(3), ferret(1)

AUTHOR
    Pierre Rioux,
    Tim Littlejohn (Project Management),
    Organelle Genome Megasequencing Project, Jun. 1994.