[ensembl-dev] program 'translate'?

Chen Jinfeng jfchen at genetics.ac.cn
Fri Nov 26 02:52:40 GMT 2010


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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