[Bioperl-l] use Bio::Search::Tiling::MapTiling

Mark A. Jensen maj at fortinbras.us
Tue Nov 16 01:08:25 UTC 2010


Hi Wei, 
You'll need to install the trunk code to access this method; the "release" is woefully out of date (not that I'm helping much on that these days). Use git to obtain the latests bioperl-live and bioperl-run from https://github.com/bioperl/, or the synchronized repos
http://repo.or.cz/w/bioperl-live.git
http://repo.or.cz/w/bioperl-run.git
cheers, 
MAJ
----- Original Message ----- 
  From: Shao, Wei (NIH/NCI) [C] 
  To: Mark A Jensen 
  Sent: Monday, November 15, 2010 10:47 AM
  Subject: use Bio::Search::Tiling::MapTiling


Dear Dr. Jensen, I am looking for a bioperl module that can be used to concatenate HSP from a blast into a sequence. I found that your Bio::Search::Tiling::MapTilingcan do exactly that. I used your example script to test it. I got an error message:“Can't locate object method "get_tiled_alns" via package "Bio::Search::Tiling::MapTiling" at get_hsp.pl line 29, <GEN1> line 2630”.It seems that method “get_tiled_alns” is not in the bioperl we installed. Is that possible? The script I used is this one:  use Bio::SearchIO;use Bio::Search::Tiling::MapTiling # Note that to get one hit, the user first blasts# the set of contigs against single sequence, the reference sequence.# The result of this BLAST run is in 'contig_tile.bls' $blio = Bio::SearchIO->new( -file => 'contig_tile.bls');$result = $blio->next_result;$hit = $result->next_hit;$tiling = Bio::Search::Tiling::MapTiling->new($hit);@alns = $tiling->get_tiled_alns('query'); # here's the concatenation:$concat_seq_obj = $alns[0]->get_seq_by_id('query'); 

  Best regards,

   

   

  Wei Shao, Ph.D. [Contractor] 
  Bioinformatics Analyst IV

  Advanced Biomedical Computing Center/HIV Drug Resistance Program
  SAIC-Frederick, Inc. 

  National Cancer Institute at Frederick
  P.O. Box B, Frederick, MD 21702
  Phone: 301/846-6021

  Fax:  301/846-6013
  Email:  shaow at mail.nih.gov


  NOTICE:  This communication may contain privileged or other confidential information.  If you are not the intended recipient, or believe that you have received this communication in error, please do not print, copy, retransmit, disseminate or otherwise use the information.  Please indicate to the sender that you have received this email in error and delete the copy you received.

   




More information about the Bioperl-l mailing list