[Bioperl-l] Multiline Query Name in Blast Output

[Jason Stajich]

does the rest show up in $r->query_description ?

-jason
On Aug 18, 2005, at 4:57 PM, Waibhav Tembe wrote:

> Hello List,
>
> Is there any way to read multi-line query name from BLAST output  
> using SearchIO?
>
> E.g., for the first few lines of BLAST output (attached at the end)  
> the code :
>
> while($result = $in->next_result ) {
>     print $result->query_name, "\n";
> }
>
> prints only :
> Cand_Start_41225:End_41249:Length_25:Extended_Length_75:Start_4
>
> How to print the entire name that is in multiple lines? i.e.,
> Cand_Start_41225:End_41249:Length_25:Extended_Length_75:Start_41200:En 
> d_41274_Section1To75_Start:12_Length:36
>
> Thanks.
>
> ------------------------
>
> BLASTN 2.2.10 [Oct-19-2004]
>
>
> Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.  
> Schaffer,
> Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
> "Gapped BLAST and PSI-BLAST: a new generation of protein database  
> search
> programs",  Nucleic Acids Res. 25:3389-3402.
>
> Query= Cand_Start_41225:End_41249:Length_25:Extended_Length_75:Start_4
> 1200:End_41274_Section1To75_Start:12_Length:36
>         (36 letters)
>
> Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
> GSS,environmental samples or phase 0, 1 or 2 HTGS sequences)
>           2,718,617 sequences; 12,254,801,043 total letters
>
> Searching..................................................done
>
>                                                                  
> Score    E
> Sequences producing significant alignments:                       
> (bits) Value
>
> gi|21956769|gb|AE013611.1| Yersinia pestis KIM section 11 of  
> 415...    59   1e-07
> gi|45434720|gb|AE017127.1| Yersinia pestis biovar Medievalis  
> str...    59   1e-07
> gi|15978115|emb|AJ414141.1| Yersinia pestis strain CO92  
> complete...    59   1e-07
>
>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/