NAME

       gt-cds - Add CDS (coding sequence) features to exon features given in GFF3 file.

SYNOPSIS

       gt cds [option ...] [GFF3_file]

OPTIONS

       -minorflen
           set the minimum length an open reading frame (ORF) must have to be added as a CDS
           feature (measured in amino acids) (default: 64)

       -startcodon
           require than an ORF must begin with a start codon (default: no)

       -finalstopcodon
           require that the final ORF must end with a stop codon (default: no)

       -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)

       -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>.

                                            10/07/2012                                  GT-CDS(1)