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getcds.pl - CDS extraction from various annotation formats


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


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

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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