GT-FINGERPRINT(1)

NAME
gt-fingerprint - Compute MD5 fingerprints for each sequence given in sequence_file(s).

SYNOPSIS

gt fingerprint [option ...] sequence_file [...]

OPTIONS

-check
    compare all fingerprints contained in the given checklist file with checksums in given sequence_files(s). The comparison is successful, if all fingerprints given in checkfile can be found in the sequence_file(s) in the exact same quantity and vice versa. (default: undefined)

-duplicates
    show duplicate fingerprints from given sequence_file(s). (default: no)

-extract
    extract the sequence(s) with the given fingerprint from sequence_file(s) and show them on stdout. (default: undefined)

-width
    set output width for FASTA sequence printing (0 disables formatting) (default: 0)

-o
    redirect output to specified file (default: undefined)

-gzip
    write gzip compressed output file (default: no)

-bzip2
    write bzip2 compressed output file (default: no)

-force
    force writing to output file (default: no)

-help
    display help and exit

-version
    display version information and exit

DESCRIPTION

If neither option -check nor option -duplicates is used, the fingerprints for all sequences are shown on stdout.

Examples:

Compute (unified) list of fingerprints:

    $ gt fingerprint U89959_ests.fas | sort | uniq > U89959_ests.checklist_uniq

Compare fingerprints:

    $ gt fingerprint -check U89959_ests.checklist_uniq U89959_ests.fas
    950b7715ab6cc030a8c810a0dba2dd33 only in sequence_file(s)

Make sure a sequence file contains no duplicates (not the case here):

    $ gt fingerprint -duplicates U89959_ests.fas
    950b7715ab6cc030a8c810a0dba2dd33        2
    gt fingerprint: error: duplicates found: 1 out of 200 (0.500%)

Extract sequence with given fingerprint:

    $ gt fingerprint -extract 6d3b4b9db4531cda588528f2c69c0a57 U89959_ests.fas
    >SQ;8720010
    TTTTTTTTTTTTTTTTTCCTGACAAAACCCCAAGACTCAATTTAATCAATCCTCAAATTTACATGATACCAACGTAATG
    GGAGCTTAAAAATA

Return values:

    0  everything went fine (-check: the comparison was successful;
                             -duplicates: no duplicates found)
    1  an error occured     (-check: the comparison was not successful;
                             -duplicates: duplicates found)

AUTHOR

Report bugs to <gt-users@genometools.org>.