---
name: "getcds.pl"
section: "1"
platform: "linux"
package: "murasaki-common"
version: "1.68.6-14"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/getcds.pl"
---

# getcds.pl(1)

CDS extraction from various annotation formats

## 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