[ensembl-dev] program 'translate'?

[Bronwen Aken]

Hi Jinfeng Chen,

I think this comes from Sean Eddy's Squid package, which you can download here:
ftp://selab.janelia.org/pub/software/squid/

Cheers,
Bronwen


On 26 Nov 2010, at 02:52, Chen Jinfeng wrote:

> Hi All,
>  
> Does any one know a program 'translate' with an option -m? It was used in Bio::EnsEMBL::Analysis::Tools::TranslateTools.pm. Runing with -m means translating DNA with Met. I have no idea where this program from. Maybe you have familiar with this program or gramene genebuilder pipeline. Tell me somethings. Thanks.
>  
> Sincerely,
> Jinfeng Chen
>  
>  
>     my $command;
>     if ( $met){
>         $command = "translate -m $file |";
>     }
>     else{
>         $command = "translate $file |";
>     }
>     open ( ORF, $command ) || die( "Error running translate" );
>     ############################################################
>     # out put is of the form:
>     #> gi|20070124|ref|NM_000918.2|.44    length 62, nt 2236..2051
>     #AHDRRRSPGLREGEGPGLCRAPGLAATSSSSRHGGHPDRIRKSPFTQKCKSHDQSWRHCRRY
>     #> gi|20070124|ref|NM_000918.2|.45    length 34, nt 2047..1946
>     #VTMSSPAPSLPHGGQASPRRPGQGGTNTLMSKNV
>     #> gi|20070124|ref|NM_000918.2|.46    length 34, nt 1942..1841
>     #KSHRRNFQKEEKPPAGGRQRDSEHGSKHSGQTHV
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