DESCRIPTION¶
-trans_table [value]
NCBI translation table number, choose from:
•1: Standard
•2: Vertebrate Mitochondrial
•3: Yeast Mitochondrial
•4: Mold Mitochondrial; Protozoan Mitochondrial;
Coelenterate Mitochondrial; Mycoplasma; Spiroplasma
•5: Invertebrate Mitochondrial
•6: Ciliate Nuclear; Dasycladacean Nuclear;
Hexamita Nuclear
•9: Echinoderm Mitochondrial; Flatworm
Mitochondrial
•10: Euplotid Nuclear
•11: Bacterial, Archaeal and Plant Plastid
•12: Alternative Yeast Nuclear
•13: Ascidian Mitochondrial
•14: Alternative Flatworm Mitochondrial
•15: Blepharisma Macronuclear
•16: Chlorophycean Mitochondrial
•21: Trematode Mitochondrial
•22: Scenedesmus obliquus Mitochondrial
•23: Thraustochytrium Mitochondrial
•24: Pterobranchia Mitochondrial
•25: Candidate Division SR1 and Gracilibacteria
(default: 1)
-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)
-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.
