[Bioperl-l] Multiline Query Name in Blast Output

[Jason Stajich]

exactly.  The line-wrap (\n) is considered whitespace as well so  
hence the separation.

On Aug 22, 2005, at 11:50 AM, Waibhav Tembe wrote:

> 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/
>>
>>
>
>

--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/