[Bioperl-l] blastall problem

DeeGee gdorjee at hotmail.com
Thu Apr 5 23:26:16 EDT 2007


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]
HLSAQKASVGPESVSGLGTRTWPRVSCEVTVQCWPGCHLKVGGFKMAPWQGVGRRPWFLTWGPLCGAASVSPSMTVASSQ
QGWDCTAGRRWLGEGEIEALAQVSEFKTVLSFQGPAASPDGSSATRVPQDVTQGPGATGGKEDSGMIPLAGTAPGAEGPA
PGDSQAVRPYKQEPSSPPLAPGLPAFLAAPGTTSCPECGKTSLKPAHLLRHRQSHSGEKPHACPECGKAFRRKEHLRRHR
DTHPGSPGSPGPALRPLPAREKPHACCECGKTFYWREHLVRHRKTHSGARPFACWECGKGFGRREHVLRHQRIHGRAAAS
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
> 
> 

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