[Bioperl-l] blastall problem

[Bernd Web]

Hi Dorjee,

Do you now use complete file paths everywhere (instead of some
relative paths that were in your script).  Did you check all read and
execute permission (turn r, x on for group and others)? And regarding
the fasta file I'd suggest closing the filehandle after you printed
the fasta sequence to the file.

open(OUTPUT,">result/fasta.faa"); #don't use this relative path and
use the "die" as was suggested earlier.
.... your other code lines
print OUTPUT
"$desc\n$seqo\n";
close(OUTPUT); #close the file.

Also check if your complete script runs from the command-line as to be
sure your problems are not related to the webserver enviroment.


BTW I do think you do not want to parse your fasta file like you do:
if ($fasta_file =~ /^(\>.+)\s+/){$desc=$1;}
$fasta_file=~s/[\n\r]//g;
if ($fasta_file =~ /([A-Z]{10}.+)/){$seqo=$1;}

$seqo will contain the description as well, so your sequence starts
with the description.
BioPerl provides code for fasta file parsing too ;-) If you really
want to stick to your code you can catch the $desc and $seqo in one
RegExp, or replace this line:
if ($fasta_file =~ /^(\>.+)\s+/){$desc=$1;}
with
if ($fasta_file =~ s/^(\>.+)\s+//){$desc=$1;}


I hope you will get your script working now.

Regards,
Bernd

On 4/6/07, Jason Stajich <jason at bioperl.org> wrote:
> 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]
> 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
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> --
> View this message in context:
> http://www.nabble.com/blastall-problem-tf3527412.html#a9867402
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> --
> Jason Stajich
> Miller Research Fellow
> University of California, Berkeley
> lab: 510.642.8441
> http://pmb.berkeley.edu/~taylor/people/js.htmlhttp://fungalgenomes.org/
>
>
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