gt-extractfeat - Online in the Cloud

PROGRAM:

NAME

gt-extractfeat - Extract features given in GFF3 file from sequence file.

SYNOPSIS

gt extractfeat [option ...] [GFF3_file]

DESCRIPTION

-type [string]
set type of features to extract (default: undefined)

-join [yes|no]
join feature sequences in the same subgraph into a single one (default: no)

-translate [yes|no]
translate the features (of a DNA sequence) into protein (default: no)

-seqid [yes|no]
add sequence ID of extracted features to FASTA descriptions (default: no)

-target [yes|no]
add target ID(s) of extracted features to FASTA descriptions (default: no)

-coords [yes|no]
add location of extracted features to FASTA descriptions (default: no)

-retainids [yes|no]
use ID attributes of extracted features as FASTA descriptions (default: no)

-gcode [value]
specify genetic code to use (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)

-v [yes|no]
be verbose (default: no)

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

-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

Genetic code numbers for option -gcode:

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

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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