[Bioperl-l] parsing xml output

Hubert Prielinger hubert.prielinger at gmx.at
Fri May 19 17:30:20 EDT 2006


ok, thanks,
it appears that I only need the species where the Protein is derived 
from, so I guess Bio:Species would satisfy me, or?
and it would work that I just pull off the accession from the blast 
output file and then assign the accession code and get as return value  
the  species name.
is it possible to just assign the accession code, because I looked up 
but they were always talking of the entire file.

regards
>
>
> Christopher Fields wrote:
>> You'll have to pull the GI or accession from each hit and do a lookup 
>> by either grabbing the sequence and using Bio::Species or use 
>> Bio::DB::Taxonomy; there isn't any tax information directly 
>> incorporated into BLAST reports AFAIK.
>>
>> Chris
>>
>> ---- Original message ----
>>  
>>> Date: Fri, 19 May 2006 10:52:28 -0600
>>> From: Hubert Prielinger <hubert.prielinger at gmx.at>  Subject: Re: 
>>> [Bioperl-l] parsing xml output  To: Warren Gish 
>>> <gish at watson.wustl.edu>, bioperl-l at bioperl.org
>>>
>>> hi,
>>> I wondered whether is it also possible in the xml output (either WU 
>>> or NCBI - Blast) to get the species (taxononmy) for every hit, if I 
>>> do a general search.
>>> regards
>>>
>>> Warren Gish wrote:
>>>    
>>>> Right, the WU-BLAST tabbed output contains more fields.  (See 
>>>> http:// blast.wustl.edu/blast/tabular.html).
>>>> --Warren
>>>>
>>>>        
>>>>> Whoops - sorry Warren - for some reason I had it in my mind that 
>>>>> it  was different.  So the blastxml parser should work fine.  The  
>>>>> WUBLAST tab-delimited output is different than NCBI's -m8/9 
>>>>> though,  right?
>>>>>
>>>>> -jason
>>>>>             
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>>>>
>>>>         
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>     
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>>   
>
>



More information about the Bioperl-l mailing list