[Bioperl-l] blastall problem

Jason Stajich jason at bioperl.org
Fri Apr 6 11:42:41 EDT 2007


When/How are are you writing your sequences to this file result.faa?   
are you using seqIO or bioperl to write the sequence  to a file?
I'm wondering if this is I/O buffering problem.

On Apr 5, 2007, at 8:26 PM, DeeGee wrote:

>
> hi Torsten,
> blastall -p blastp -i result/fasta.faa -d /export/home/database/nr  
> works
> perfectly fine on the command line, and the 'fasta.faa' is in fasta  
> format:
>
>> gi|18676474|dbj|BAB84889.1| FLJ00134 protein [Homo sapiens]
> HLSAQKASVGPESVSGLGTRTWPRVSCEVTVQCWPGCHLKVGGFKMAPWQGVGRRPWFLTWGPLCGAASV 
> SPSMTVASSQ
> QGWDCTAGRRWLGEGEIEALAQVSEFKTVLSFQGPAASPDGSSATRVPQDVTQGPGATGGKEDSGMIPLA 
> GTAPGAEGPA
> PGDSQAVRPYKQEPSSPPLAPGLPAFLAAPGTTSCPECGKTSLKPAHLLRHRQSHSGEKPHACPECGKAF 
> RRKEHLRRHR
> DTHPGSPGSPGPALRPLPAREKPHACCECGKTFYWREHLVRHRKTHSGARPFACWECGKGFGRREHVLRH 
> QRIHGRAAAS
> AQGAVAPGPDGGGPFPPWPLG
>
> it seems like i'm just one bloody step away from success. ^ ^*  
> can't figure
> out the prob.
> thanks for your help.
>
>
> Torsten Seemann wrote:
>>
>> Dorjee,
>>
>>> thanks alot for your reply again. as per your suggestion (using 'die
>>> "could
>>> not get seq" if not defined $queryin;'), i now get the following  
>>> error
>>> message:
>>> Software error:
>>> could not get seq at /usr/local/apache2/htdocs/remote_ncbi.pl  
>>> line 50.
>>> i've attached the script. could you plz have a look at it and see  
>>> where
>>> am i
>>> going wrong.
>>> cheers mate!
>>
>> This strongly suggests that your FASTA file is not actually in FASTA
>> format.
>> http://en.wikipedia.org/wiki/Fasta_format
>>
>> Does it work if you pass it to blastall on the command line?
>> eg. blastall -p blastp -i result/fasta.faa -d /export/home/ 
>> database/nr
>>
>>> Saier Lab.
>>> 858-534-2457
>>
>> Are you working at UCSD?
>>
>> --Torsten
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
>
> -- 
> View this message in context: http://www.nabble.com/blastall- 
> problem-tf3527412.html#a9867402
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
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--
Jason Stajich
Miller Research Fellow
University of California, Berkeley
lab: 510.642.8441
http://pmb.berkeley.edu/~taylor/people/js.html
http://fungalgenomes.org/

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