GT-ID_TO_MD5(1)

NAME
gt-id_to_md5 - Change sequence IDs in given GFF3 files to MD5 fingerprints of the corresponding sequences.

SYNOPSIS

gt id_to_md5 [option ...] [GFF3_file ...]

OPTIONS

-seqfile
    set the sequence file from which to extract the features (default: undefined)

-seqfiles
    set the sequence files from which to extract the features use -- to terminate the list of sequence files

-matchdesc
    match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) (default: no)

-usedesc
    use sequence descriptions to map the sequence IDs (in GFF3) to actual sequence entries. If a description contains a sequence range (e.g., III:1000001..2000000), the first part is used as sequence ID (III) and the first range position as offset (1000001) (default: no)

-regionmapping
    set file containing sequence-region to sequence file mapping (default: undefined)

-subtargetids
    substitute the target IDs with MD5 sums (default: yes)

-v
    be verbose (default: no)

-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

File format for option -regionmapping:

The file supplied to option -regionmapping defines a “mapping”. A mapping maps the sequence-regions given in the GFF3_file to a sequence file containing the corresponding sequence. Mappings can be defined in one of the following two forms:

mapping = { chr1 = "hs_ref_chr1.fa.gz", chr2 = "hs_ref_chr2.fa.gz" }

or

function mapping(sequence_region) return "hs_ref_"..sequence_region..".fa.gz" end

The first form defines a Lua (http://www.lua.org/) table named “mapping” which maps each sequence region to the corresponding sequence file. The second one defines a Lua function “mapping”, which has to return the sequence file name when it is called with the sequence_region as argument.

AUTHOR

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