gt-cds(1) Add CDS (coding sequence) features to exon features given in GFF3 file.

SYNOPSIS

gt cds [option ...] [GFF3_file]

DESCRIPTION

-minorflen [value]

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 [yes|no]

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

-finalstopcodon [yes|no]

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

-seqfile [filename]

set the sequence file from which to take the sequences (default: undefined)

-encseq [filename]

set the encoded sequence indexname from which to take the sequences (default: undefined)

-seqfiles

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

-matchdesc [yes|no]

search the sequence descriptions from the input files for the desired sequence IDs (in GFF3), reporting the first match (default: no)

-matchdescstart [yes|no]

exactly match the sequence descriptions from the input files for the desired sequence IDs (in GFF3) from the beginning to the first whitespace (default: no)

-usedesc [yes|no]

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 [string]

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

-v [yes|no]

be verbose (default: no)

-o [filename]

redirect output to specified file (default: undefined)

-gzip [yes|no]

write gzip compressed output file (default: no)

-bzip2 [yes|no]

write bzip2 compressed output file (default: no)

-force [yes|no]

force writing to output file (default: no)

-help

display help and exit

-version

display version information and exit

File format for option -regionmapping:

The file supplied to option -regionmapping defines a "mapping". A mapping maps the sequence-region entries 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.

REPORTING BUGS

Report bugs to <[email protected]>.

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