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getcds.pl - Online in the Cloud

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

This is the command getcds.pl 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


getcds.pl - CDS extraction from various annotation formats

SYNOPSIS


getcds.pl [options] input file [output file] [input file [outputfile] ...]

OPTIONS


Options include:
redirect => Enable a redirect at runtime. explained below.
force => allows writing empty .cds files

If [output file] is unspecificied, "[input file].cds" is used.

There's lots of dark magic that can be performed with .redirect files. Redirects are used
to modify the ordinary behaviour and can be applied on a global basis (a .redirect file in
the same directory as [input file]), and/or on a per-input basis ([input file].redirect).
Redirects are read in that order such that per-input effects are applied ontop of global
effects.

If you've left the filename as-is from an Ensembl downoad, the appropriate Ensembl DB
source will be guessed automatically.

Possible redirects:

CDS - changes what tag type is searched for when running on bioperl files (default is CDS)
offset - add some value to all coordinates
+bioperl - on top of any other redirect-based data, also extract annotation via bioperl
(using a direct disables bioperl's parser by default)
ensembl_build - grab data from the ensembl (in the specified schema)
ucsc_build - grab data from (in the specified schema)
murasaki_synth - synthesize annotation data for each anchor from an alignment (if this is
a directory, then each input file (eg input.lav) is checked for a corresponding .anchors
file (eg. input.anchors).
primary - what to type of tags to create from data gathered from outside data (eg:
ensembl, ucsc, or murasaki). default is the same as the cds redirect.
chromosome - forces a specific chromosome rather than deriving from filename
gtf - extract annotation from a .gtf file

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