gt-extractfeat1

Usage

Overview

-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.