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