mapping = {
  chr1  = "hs_ref_chr1.fa.gz",
  chr2  = "hs_ref_chr2.fa.gz"
}
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:
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 https://github.com/genometools/genometools/issues.