EnglishFrenchSpanish

Ad


OnWorks favicon

faidx - Online in the Cloud

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

This is the command faidx 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


faidx - Fetch sequences from FASTA

SYNOPSIS


faidx [-h] [-b BED] [-o OUT] [-i {bed,chromsizes,nucleotide,transposed}] [-c] [-r] [-n |
-f] [-x] [-l] [-s DEFAULT_SEQ] [-d DELIMITER] [-g REGEX] [-m | -M] [--version] fasta
[regions [regions ...]]

DESCRIPTION


Fetch sequences from FASTA. If no regions are specified, all entries in the input file are
returned. Input FASTA file must be consistently line-wrapped, and line wrapping of output
is based on input line lengths.

OPTIONS


Positional arguments
fasta FASTA file

regions
space separated regions of sequence to fetch e.g. chr1:1-1000

Optional arguments
-h, --help
show this help message and exit

-b BED, --bed BED
bed file of regions

-o OUT, --out OUT
output file name (default: stdout)

-i {bed,chromsizes,nucleotide,transposed}, --transform
{bed,chromsizes,nucleotide,transposed}
transform the requested regions into another format. default: None

-c, --complement
complement the sequence. default: False

-r, --reverse
reverse the sequence. default: False

-n, --no-names
omit sequence names from output. default: False

-f, --full-names
output full names including description. default: False

-x, --split-files
write each region to a separate file (names are derived from regions)

-l, --lazy
fill in --default-seq for missing ranges. default: False

-s DEFAULT_SEQ, --default-seq DEFAULT_SEQ
default base for missing positions and masking. default: N

-d DELIMITER, --delimiter DELIMITER
delimiter for splitting names to multiple values (duplicate names will be
discarded). default: None

-g REGEX, --regex REGEX
regular expression for filtering non-matching sequence names. default: .*

-m, --mask-with-default-seq
mask the FASTA file using --default-seq default: False

-M, --mask-by-case
mask the FASTA file by changing to lowercase. default: False

--version
print pyfaidx version number

Use faidx online using onworks.net services


Free Servers & Workstations

Download Windows & Linux apps

  • 1
    DivFix++
    DivFix++
    DivFix++ is yours AVI video repair and
    preview software. It designed for repair
    and preview files which are on download
    from ed2k(emule), torrent, gnutella, ftp...
    Download DivFix++
  • 2
    JBoss Community
    JBoss Community
    Community driven projects featuring the
    latest innovations for cutting edge
    apps. Our flagship project JBoss AS is
    the leading Open Source,
    standards-compliant...
    Download JBoss Community
  • 3
    Django Filer
    Django Filer
    django Filer is a file management
    application for django that makes
    handling files and images a breeze.
    django-filer is a file management
    application for djang...
    Download Django Filer
  • 4
    xCAT
    xCAT
    Extreme Cluster Administration Toolkit.
    xCAT is a scalable cluster management
    and provisioning tool that provides
    hardware control, discovery, and OS
    diskful/di...
    Download xCAT
  • 5
    Psi
    Psi
    Psi is cross-platform powerful XMPP
    client designed for experienced users.
    There are builds available for MS
    Windows, GNU/Linux and macOS.. Audience:
    End Users...
    Download Psi
  • 6
    Blobby Volley 2
    Blobby Volley 2
    Official continuation of the famous
    Blobby Volley 1.x arcade game..
    Audience: End Users/Desktop. User
    interface: OpenGL, SDL. Programming
    Language: C++, Lua. C...
    Download Blobby Volley 2
  • More »

Linux commands

Ad