EnglishFrenchSpanish

Ad


OnWorks favicon

gt-splicesiteinfo - Online in the Cloud

Run gt-splicesiteinfo in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command gt-splicesiteinfo 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-splicesiteinfo - Show information about splice sites given in GFF3 files.

SYNOPSIS


gt splicesiteinfo [option ...] [GFF3_file ...]

DESCRIPTION


-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)

-addintrons [yes|no]
add intron features between existing exon features (before computing the information
to be shown) (default: no)

-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.

REPORTING BUGS


Report bugs to <[email protected]>.

Use gt-splicesiteinfo online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    OfficeFloor
    OfficeFloor
    OfficeFloor provides inversion of
    coupling control, with its: - dependency
    injection - continuation injection -
    thread injection For more information
    visit the...
    Download OfficeFloor
  • 2
    DivKit
    DivKit
    DivKit is an open source Server-Driven
    UI (SDUI) framework. It allows you to
    roll out server-sourced updates to
    different app versions. Also, it can be
    used fo...
    Download DivKit
  • 3
    subconverter
    subconverter
    Utility to convert between various
    subscription format. Shadowrocket users
    should use ss, ssr or v2ray as target.
    You can add &remark= to
    Telegram-liked HT...
    Download subconverter
  • 4
    SWASH
    SWASH
    SWASH is a general-purpose numerical
    tool for simulating unsteady,
    non-hydrostatic, free-surface,
    rotational flow and transport phenomena
    in coastal waters as ...
    Download SWASH
  • 5
    VBA-M (Archived - Now on Github)
    VBA-M (Archived - Now on Github)
    Project has moved to
    https://github.com/visualboyadvance-m/visualboyadvance-m
    Features:Cheat creationsave statesmulti
    system, supports gba, gbc, gb, sgb,
    sgb2Tu...
    Download VBA-M (Archived - Now on Github)
  • 6
    Stacer
    Stacer
    Linux System Optimizer and Monitoring
    Github Repository:
    https://github.com/oguzhaninan/Stacer.
    Audience: End Users/Desktop. User
    interface: Qt. Programming La...
    Download Stacer
  • More »

Linux commands

Ad