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