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This is the command gt-extractfeat that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

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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