[Bioperl-l] Multiline Query Name in Blast Output

[Waibhav Tembe]

Thanks Jason. The rest showed up in $r->description. Is there any reason 
for this?

Does BioPerl assume that first whit-space character separates the query 
name and description?



Jason Stajich wrote:

> 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/
>