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
    SAGA GIS
    SAGA GIS
    SAGA - System for Automated
    Geoscientific Analyses - is a Geographic
    Information System (GIS) software with
    immense capabilities for geodata
    processing and ana...
    Download SAGA GIS
  • 2
    Toolbox for Java/JTOpen
    Toolbox for Java/JTOpen
    The IBM Toolbox for Java / JTOpen is a
    library of Java classes supporting the
    client/server and internet programming
    models to a system running OS/400,
    i5/OS, o...
    Download Toolbox for Java/JTOpen
  • 3
    D3.js
    D3.js
    D3.js (or D3 for Data-Driven Documents)
    is a JavaScript library that allows you
    to produce dynamic, interactive data
    visualizations in web browsers. With D3
    you...
    Download D3.js
  • 4
    Shadowsocks
    Shadowsocks
    A fast tunnel proxy that helps you
    bypass firewalls This is an application
    that can also be fetched from
    https://sourceforge.net/projects/shadowsocksgui/.
    It ha...
    Download Shadowsocks
  • 5
    GLPI Themes
    GLPI Themes
    Download release at
    https://github.com/stdonato/glpi-modifications/
    Color themes for GLPI 0.84 and 0.85 New
    Modifications for GLPI This is an
    application that c...
    Download GLPI Themes
  • 6
    SMPlayer
    SMPlayer
    SMPlayer is a free media player for
    Windows and Linux with built-in codecs
    that can also play YouTube videos. One
    of the most interesting features of
    SMPlayer:...
    Download SMPlayer
  • More »

Linux commands

Ad