[ensembl-dev] program 'translate'?

Chen Jinfeng jfchen at genetics.ac.cn
Fri Nov 26 09:54:24 GMT 2010


Hi Bronwen,

I tried Squid package just now. It works fine. Thank you very much for the information.
Have a nice weekend!

Sincerely,
Jinfeng


From: Bronwen Aken 
Sent: Friday, November 26, 2010 5:37 PM
To: Chen Jinfeng 
Cc: dev at ensembl.org 
Subject: Re: [ensembl-dev] program 'translate'?


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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