Standalone Blast

[Nandu123]

Does anyone help me with the script of standalone blast that will execute the blastn, blastp and tblastx, with one script and e values, and hits, and score

[numberwhun]

Does anyone help me with the script of standalone blast that will execute the blastn, blastp and tblastx, with one script and e values, and hits, and score

This is the Perl forum. I do not know what blastn, blastp, and tblastx are and your question is extremely vague and not well worded. If you could further explain what you are looking for, that would be most helpful. At this point, I don't know how the Perl forum can further help you.

Regards,

Jeff

[KevinADC]

Does anyone help me with the script of standalone blast that will execute the blastn, blastp and tblastx, with one script and e values, and hits, and score

look into bioperl: www.bioperl.org

or search CPAN: search.cpan.org

[numberwhun]

look into bioperl: www.bioperl.org

or search CPAN: search.cpan.org

You have either had exposure to that or have played with it because I hadn't a clue what they were talking about.

[Nandu123]

Hello masters!!!!!!!!!
I hope my script is a bioperl script which is related to perl of course,,,,, so should be included in the perl forum I suppose,,,,, and standalone blast is a means to use blast locally using perl/ bioperl script. So I asked it here. Again, I am facing few bugs with the "my" thus, if someone can help me,,,, to get it debug, will be great!!!!!!!

My script is as follows:

#!/usr/bin/perl -w
use strict;
 
# Local-blast "factory object" creation and blast-parameter:
 
 
 # initialization:
use Bio::Tools::Run::StandAloneBlast;
use Bio::SeqIO;
use Bio::Seq;
use Bio::SearchIO;
 
# Process Command line arguments
if(scalar @ARGV !=6){
  my $usage = " ./home/blaststd.pl INPUTFILE BLASTDB PROGRAM E-CUTOFF OUTPUTFILE";
   print  "Wrong number of arguments\n";
   die "$usage\n";
   }
#the filenames containing input sequence
my $input_seq1 = dna.fasta;
my $input_seq2 = sequences.fasta;
   $input_seq1 = $ARGV[0];
   $input_seq2 =$ARGV[1];
#the database to blast against
my $db = $ARGV[2];
# the blast program to use
my $program = $ARGV[3];
#the expect value (Evalue)cutoff
my $cutoff = $ARGV[4];
#the name of the output file
my $output_file = $ARGV [5];
#blast parameters with type of programs, type of database, type of file, type of method:
 
my @params1= ('programs'=> 'blastn','database' => 'ecoli.nt','outfile' =>'blastn.out','e 1e-10',
    '_READMETHOD' => 'Blast');
my @params2= ('programs'=> 'blastp','database' => 'ecoli.aa','outfile' =>'blastp.out','e 1e-10',
   '_READMETHOD' => 'Blast');
my @params3 = ('programs'=> 'tblastx','database' => 'ecoli.nt','outfile' =>'blastx.out','e 1e-10',
    '_READMETHOD' => 'Blast');
 
print "Enter the type of program";
 
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params1, @params2, @params3);
 
 
 # Blast a sequence against a database:
 
 
   my $in1 = Bio::SeqIO->new(-file=>'dna.fasta' , -format =>'Fasta');
   my $in2= Bio::SeqIO->new(-file=>'sequences.fasta',-format=>'Fasta');
 
# Load the sequence into a Bio::Seq obj
   my  $seq =Bio::Seq->new($in1->next_seq());
   my $seq2 =Bio::Seq->new($in2->next_seq());
 
#my  $input2 = $str->next_seq();
my  $blast_report = $factory->blastall($seq,$seq2);
 
 
 
 
 
 
 
 
# Blast a sequence against a database:
# format can be , 'blast', 'exonerate', ...
 
my $searchio1 = new Bio::SearchIO(-format => 'blastn',
                                     -file => 'dna.fasta');
my $searchio2= new Bio::SearchIO(-format => 'blastp',-file => 'sequences.fasta');
my $searchio3 = new Bio::SearchIO(-format => 'tblastx' -file => 'dna.fasta')
 
while  (my $result = $searchio->next_result)
    {
 
       while(my $hit = $result->next_hit) 
    {
 
        # process the Bio::Search::Hit::HitI object
           while(my $hsp = $hit->next_hsp )
          {
        # process the Bio::Search::HSP::HSPI object
          if($hsp->length('total') >=. 75) 
            {
             print "Hit=", $hit->name,
                   "len=",$hsp->length('total'),
                   "percent_id=",$hsp->percent_identity,
                   "Score =", my $bitsore->bits(%s),
                   "Expected value=", my $evalue,"\n";
                }
               }
            }
       }
 }
print "Thank you.\n";
 

[KevinADC]

You have either had exposure to that or have played with it because I hadn't a clue what they were talking about.

I have seen this question or similar asked on other forums so I have some knowledge of what it is. I have no practical experience with it though.

[KevinADC]

You ned to quote barewords, like here:

my $input_seq1 = dna.fasta;
my $input_seq2 = sequences.fasta;
 

should be:

my $input_seq1 = 'dna.fasta';
my $input_seq2 = 'sequences.fasta';
 

see if that helps gets things working. If not, post the exact error messages you are getting when trying your code. I do not have any of the modules you are using installed so I can't help debug the syntax except by "eye", which I am not prepared to do.

[nb175]

hi, I need help with my blast script. I need to specify that i need only the first ten hits, any idea how i could go about that?Thanks. here;s the script

#! /usr/bin/perl
use warnings;
use strict;

use Bio::SeqIO;
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;

my $seqio_obj;
my $seq_obj;
my @params;
my $blast_obj;
my $result_obj;
my $report_obj;

$seqio_obj = Bio::SeqIO->new(-file => 'seq.fasta',
-format => 'fasta' );
# to wrtie the sequence to afasta file
$seq_obj = $seqio_obj->next_seq;
#print $seq_obj->seq,"\n";
@params = (program => 'blastp',
database => 'pdbaa',
outfile => 'blast1.out');
$blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
$report_obj = $blast_obj->blastall($seq_obj);
$result_obj = $report_obj->next_result;
print $result_obj->num_hits;