EnglishFrenchSpanish

Ad


OnWorks favicon

locuspocus - Online in the Cloud

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

This is the command locuspocus 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


locuspocus - calculate locus coordinates for the given gene annotation

SYNOPSIS


locuspocus [options] gff3file1 [gff3file2 gff3file3 ...]

DESCRIPTION


Basic options:

-d|--debug
print detailed debugging messages to terminal (standard error)

-h|--help
print this help message and exit

-v|--version
print version number and exit

iLocus parsing:

-l|--delta: INT
when parsing interval loci, use the following delta to extend gene loci and include
potential regulatory regions; default is 500

-s|--skipends
when enumerating interval loci, exclude unannotated (and presumably incomplete)
iLoci at either end of the sequence

-e|--endsonly
report only incomplete iLocus fragments at the unannotated ends of sequences
(complement of --skipends)

-y|--skipiiloci
do not report intergenic iLoci

Refinement options:

-r|--refine
by default genes are grouped in the same iLocus if they have any overlap; 'refine'
mode allows for a more nuanced handling of overlapping genes

-c|--cds
use CDS rather than UTRs for determining gene overlap; implies 'refine' mode

-m|--minoverlap: INT
the minimum number of nucleotides two genes must overlap to be grouped in the same
iLocus; default is 1

Output options:

-n|--namefmt: STR
provide a printf-style format string to override the default ID format for newly
created loci; default is 'locus%lu' (locus1, locus2, etc) for loci and 'iLocus%lu'
(iLocus1, iLocus2, etc) for interval loci; note the format string should include a
single %lu specifier to be filled in with a long unsigned integer value

-i|--ilens: FILE
create a file with the lengths of each intergenic iLocus

-g|--genemap: FILE
print a mapping from each gene annotation to its corresponding locus to the given
file

-o|--outfile: FILE
name of file to which results will be written; default is terminal (standard
output)

-T|--retainids
retain original feature IDs from input files; conflicts will arise if input
contains duplicated ID values

-t|--transmap: FILE
print a mapping from each transcript annotation to its corresponding locus to the
given file

-V|--verbose
include all locus subfeatures (genes, RNAs, etc) in the GFF3 output; default
includes only locus features

Input options:

-f|--filter: TYPE
comma-separated list of feature types to use in constructing loci/iLoci; default is
'gene'

-p|--parent: CT:PT
if a feature of type $CT exists without a parent, create a parent for this feature
with type $PT; for example, mRNA:gene will create a gene feature as a parent for
any top-level mRNA feature; this option can be specified multiple times

-u|--pseudo
correct erroneously labeled pseudogenes

Use locuspocus online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    AstrOrzPlayer
    AstrOrzPlayer
    AstrOrz Player is a free media player
    software, part based on WMP and VLC. The
    player is in a minimalist style, with
    more than ten theme colors, and can also
    b...
    Download AstrOrzPlayer
  • 2
    movistartv
    movistartv
    Kodi Movistar+ TV es un ADDON para XBMC/
    Kodi que permite disponer de un
    decodificador de los servicios IPTV de
    Movistar integrado en uno de los
    mediacenters ma...
    Download movistartv
  • 3
    Code::Blocks
    Code::Blocks
    Code::Blocks is a free, open-source,
    cross-platform C, C++ and Fortran IDE
    built to meet the most demanding needs
    of its users. It is designed to be very
    extens...
    Download Code::Blocks
  • 4
    Amidst
    Amidst
    Amidst or Advanced Minecraft Interface
    and Data/Structure Tracking is a tool to
    display an overview of a Minecraft
    world, without actually creating it. It
    can ...
    Download Amidst
  • 5
    MSYS2
    MSYS2
    MSYS2 is a collection of tools and
    libraries providing you with an
    easy-to-use environment for building,
    installing and running native Windows
    software. It con...
    Download MSYS2
  • 6
    libjpeg-turbo
    libjpeg-turbo
    libjpeg-turbo is a JPEG image codec
    that uses SIMD instructions (MMX, SSE2,
    NEON, AltiVec) to accelerate baseline
    JPEG compression and decompression on
    x86, x8...
    Download libjpeg-turbo
  • More »

Linux commands

  • 1
    abi-tracker
    abi-tracker
    abi-tracker - visualize ABI changes
    timeline of a C/C++ software library.
    DESCRIPTION: NAME: ABI Tracker
    (abi-tracker) Visualize ABI changes
    timeline of a C/C+...
    Run abi-tracker
  • 2
    abicheck
    abicheck
    abicheck - check application binaries
    for calls to private or evolving symbols
    in libraries and for static linking of
    some system libraries. ...
    Run abicheck
  • 3
    couriermlm
    couriermlm
    couriermlm - The Courier mailing list
    manager ...
    Run couriermlm
  • 4
    couriertcpd
    couriertcpd
    couriertcpd - the Courier mail server
    TCP server daemon ...
    Run couriertcpd
  • 5
    gbklatex
    gbklatex
    bg5latex - Use LaTeX directly on a Big5
    encodedtex file bg5pdflatex - Use
    pdfLaTeX directly on a Big5 encodedtex
    file bg5+latex - Use LaTeX directly on a
    Big5+...
    Run gbklatex
  • 6
    gbkpdflatex
    gbkpdflatex
    bg5latex - Use LaTeX directly on a Big5
    encodedtex file bg5pdflatex - Use
    pdfLaTeX directly on a Big5 encodedtex
    file bg5+latex - Use LaTeX directly on a
    Big5+...
    Run gbkpdflatex
  • More »

Ad