[Bioperl-l] formatdb with the nr database

Hubert Prielinger hubert.prielinger at gmx.at
Mon Jan 23 20:41:35 EST 2006


hi,
sorry, but what do you mean with is your blast database in /nr...
my database is located in the path /home/Hubert/blast/blast-2.2.13/data



Nagesh Chakka wrote:

> Can you just run the blast from the command line.
> Is your blast database in "/nr".
>
> Hubert Prielinger wrote:
>
>> Hi Nagesh,
>> thank you very much, I put my database into the data folder, run the 
>> program and got the following error message:
>>
>> submit Sequence...just do it....
>> sh: /home/Hubert/blast/blast-2.2.13/bin/blastall: cannot execute 
>> binary file
>>
>> ------------- EXCEPTION  -------------
>> MSG: blastall call crashed: 32256 
>> /home/Hubert/blast/blast-2.2.13/bin/blastall -p  blastp  -d  "/nr"  
>> -i  /tmp/QTZfYMbgLM  -e  20000  -o  /tmp/v3YwWvONZ1  -v  1000  -b  1000
>>
>> STACK Bio::Tools::Run::StandAloneBlast::_runblast 
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Tools/Run/StandAloneBlast.pm:759
>> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast 
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Tools/Run/StandAloneBlast.pm:706
>> STACK Bio::Tools::Run::StandAloneBlast::blastall 
>> /usr/lib/perl5/site_perl/5.8.6/Bio/Tools/Run/StandAloneBlast.pm:557
>> STACK toplevel 
>> /home/Hubert/installed/eclipse/workspace/Database_Search/standalone_blast.pl:46 
>>
>>
>> --------------------------------------
>>
>> Why it did not find my binary file, but it is there
>>
>> regards
>>
>> Nagesh Chakka wrote:
>>
>>> Hi,
>>> The following is from the StandAloneBlast.pm documentation
>>> " If the databases which will be searched by BLAST are located in the
>>> data subdirectory of the blast program directory (the default
>>> installation location), StandAloneBlast will find them; however, if the
>>> database files are located in any other location, environmental 
>>> variable
>>> $BLASTDATADIR will need to be set to point to that directory."
>>> Please note that I have not used this module before.
>>> Nagesh
>>>
>>>
>>>
>>> On Mon, 2006-01-23 at 17:08 -0600, Hubert Prielinger wrote:
>>>  
>>>
>>>> Hi,
>>>> thank you very much for the help, another questions that raises up, 
>>>> do I have to write the path to the database files as well, I guess 
>>>> so, but how I do that, the same way I write the path to teh blast 
>>>> bin files?
>>>> Does anybody know how to set the Composition based statistics 
>>>> parameter?
>>>> there is my code:
>>>>
>>>> #!/usr/bin/perl -w
>>>>
>>>> use Bio::Tools::Run::StandAloneBlast;
>>>> use Bio::Seq;
>>>> use Bio::SeqIO;
>>>> use strict;
>>>>
>>>> BEGIN
>>>> {
>>>>    $ENV{PATH}=":/home/Hubert/blast/blast-2.2.13/bin/:";
>>>> }
>>>>
>>>>
>>>> # parameters
>>>> my $expect_value = 20000;
>>>> #my $filter_query_sequence = 'F';
>>>> my $one_line_description = 1000;
>>>> my $alignments = 1000;
>>>> # my $strands = 1;
>>>> my $count = 1;
>>>>
>>>> my @params = ('program' => 'blastp', 'database' => 'nr');
>>>> #my $progress_interval = 100;
>>>>
>>>>
>>>> my $seqio_obj = Bio::SeqIO->new(
>>>>  -file   => "Perm.txt",
>>>>  -format => "raw",
>>>> );
>>>>
>>>> # create factory object and set parameters
>>>> my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>>>>
>>>> $factory->e($expect_value);
>>>> #$factory->F($filter_query_sequence);
>>>> $factory->v($one_line_description);
>>>> $factory->b($alignments);
>>>> #$factory->S($strands);
>>>>
>>>>
>>>> # get query
>>>>
>>>> while ( my $query = $seqio_obj->next_seq ) {
>>>>      my $blast_report = $factory->blastall($query);
>>>>      my $filename = "comp_$count.txt";
>>>>      my $factory->outfile($filename);
>>>>      print $query->seq;
>>>>      print "\n";
>>>>
>>>>  $count++;
>>>> }
>>>>
>>>> thank you very much in advance
>>>> Hubert
>>>>
>>>>
>>>>
>>>> Nagesh Chakka wrote:
>>>>
>>>>  
>>>>
>>>>> Hi Hubert,
>>>>> I downloaded the nr.00.tar.gz file a week ago. I was able to get 
>>>>> the following files
>>>>> .phr, .pin, .pnd, .pni, .ppd, .ppi, .psd, .psi, .psq, .pal files. 
>>>>> I have no trouble in running standalone blast. You are not 
>>>>> required to run formardb on the downloaded blast databases and 
>>>>> that may be the reason why the sequences are not included as it 
>>>>> will also reduce the size of the file.
>>>>> Did you try to run a blast search, if so is it giving you any errors?
>>>>> Nagesh
>>>>>
>>>>>
>>>>>
>>>>> Hubert Prielinger wrote:
>>>>>
>>>>>    
>>>>>
>>>>>> Hi,
>>>>>> I have downloaded the nr database for doing a blast search 
>>>>>> locally, now I'm supposed to index the database with formatdb, 
>>>>>> but it doesn't work...
>>>>>> The online help says that you need a fasta file that is indexed 
>>>>>> to use for searching the database, but when I uncompressed the 
>>>>>> zip file, there were only .phr, .pnd, .pin, .pni, .ppd file....
>>>>>> Is there anybody who can tell me, how to use formatdb with the nr 
>>>>>> database...
>>>>>>
>>>>>> Help is very appreciated
>>>>>> Thank you very much in advance
>>>>>>
>>>>>> Hubert
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioperl-l mailing list
>>>>>> Bioperl-l at portal.open-bio.org
>>>>>> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>>>>       
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>     
>>>>
>>>>
>>>
>>>
>>>  
>>>
>>
>
>



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