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.\" ========================================================================
.\"
.IX Title "GETCDS 1"
.TH GETCDS 1 "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
getcds.pl \- CDS extraction from various annotation formats
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
getcds.pl [options] input file [output file] [input file [outputfile] ...]
.SH "OPTIONS"
.IX Header "OPTIONS"
.Vb 3
\& Options include:
\&   redirect => Enable a redirect at runtime. explained below.
\&   force => allows writing empty .cds files
.Ve
.PP
If [output file] is unspecificied, \*(L"[input file].cds\*(R" is used.
.PP
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.
.PP
If you've left the filename as-is from an Ensembl downoad, the appropriate
Ensembl \s-1DB\s0 source will be guessed automatically.
.PP
Possible redirects:
.IP "\s-1CDS\s0 \- changes what tag type is searched for when running on bioperl files (default is \s-1CDS\s0)" 4
.IX Item "CDS - changes what tag type is searched for when running on bioperl files (default is CDS)"
.PD 0
.IP "offset \- add some value to all coordinates" 4
.IX Item "offset - add some value to all coordinates"
.IP "+bioperl \- on top of any other redirect-based data, also extract annotation via bioperl (using a direct disables bioperl's parser by default)" 4
.IX Item "+bioperl - on top of any other redirect-based data, also extract annotation via bioperl (using a direct disables bioperl's parser by default)"
.IP "ensembl_build \- grab data from the ensembl (in the specified schema)" 4
.IX Item "ensembl_build - grab data from the ensembl (in the specified schema)"
.IP "ucsc_build \- grab data from (in the specified schema)" 4
.IX Item "ucsc_build - grab data from (in the specified schema)"
.IP "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)." 4
.IX Item "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)."
.IP "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." 4
.IX Item "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."
.IP "chromosome \- forces a specific chromosome rather than deriving from filename" 4
.IX Item "chromosome - forces a specific chromosome rather than deriving from filename"
.IP "gtf \- extract annotation from a .gtf file" 4
.IX Item "gtf - extract annotation from a .gtf file"