[Bioperl-l] RemoteBlast again

[Brian Osborne]

William,

The format of your input file doesn't look right. I think it should be
fasta, with lines 1 and 2 something like this:

>Adra2a NM_007417
atgggctcactgcagccggatgccggcaacagcagctggaacgggaccga

Brian O.


-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of william ritchie
Sent: Monday, January 26, 2004 3:10 AM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] RemoteBlast again

Sorry about the incomplete question, I was leaving and
I wondered if this was a common error. This is the
code that gives my previous error message....

 use strict;
use Bio::SearchIO;
use Bio::Tools::Run::RemoteBlast;
use Bio::Perl;
use Bio::SeqIO;


    my @inputfiles = @ARGV;

    foreach my $inputfile (@inputfiles)

{

         my $prog = 'blastn';
         #my $db   = 'gbEST';
         my $e_val= '1e-10';


         my @params = ( '-prog' => $prog,
                ' -data  '=> 'est_mouse',
                ' -expect'  => $e_val,
                ' -readmethod'  => ' SearchIO'  );


         my $factory =
Bio::Tools::Run::RemoteBlast->new(@params);


                          my $v = 1;


         my $str = Bio::SeqIO->new(
                        -file=>
"/home/billthebrute/Projet/endogpcr/"."$inputfile",
                      #  -format  => ' Fasta'
                                  );


$Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} =
'est_mouse';

$Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} =
'blastn';

         while (my $input = $str->next_seq())
             {


          my $r = $factory->submit_blast($input);


          print STDERR "waiting..." if( $v > 0 );

           while ( my @rids = $factory->each_rid ) {
             foreach my $rid ( @rids ) {
               my $rc =
$factory->retrieve_blast($rid);
               if( !ref($rc) ) {
                 if( $rc < 0 ) {
                   $factory->remove_rid($rid);
                 }
                 print STDERR "." if ( $v > 0 );
                 sleep 5 ;
               } else {
                 my $result = $rc->next_result();
                 #save the output
                 #my $filename =
$result->query_name()."\.out";
                 print "$inputfile";

$factory->save_output("/home/billthebrute/Projet/blasted/"."$inputfile");
                 $factory->remove_rid($rid);



               }
             }
           }
          }
}



I m recieving this error message:
----------------- WARNING ---------------------
MSG: seq doesn't validate, mismatch is 1
---------------------------------------------------

------------- EXCEPTION  -------------
MSG: Attempting to set the sequence to
[ADRA2ANM_007417ATGGGCTCACTGCAGCCGGATGCCGGCAACAGCAGCTGGAACGGGACCGAAGCGCCCGGA
GGCGGC

With the below file!
Thanks

>Adra2a
NM_007417
atgggctcactgcagccggatgccggcaacagcagctggaacgggaccga
agcgcccggaggcggcacccgagccaccccttactccctgcaggtgacac
tgacgctggtttgcctggctggcctgctcatgctgttcacagtatttggc
aacgtgctggttattatcgcggtgttcaccagtcgcgcgctcaaagctcc
ccaaaacctcttcctggtgtccctggcctcagcggacatcctggtggcca
cgctggtcattcccttttctttggccaacgaggttatgggttactggtac
tttggtaaggtgtggtgtgagatctatttggctctcgacgtgctcttttg
cacgtcgtccatagtgcacctgtgcgccatcagccttgaccgctactggt
ccatcacgcaggccatcgagtacaacctgaagcgcacgccgcgtcgcatc
aaggccatcattgtcaccgtgtgggtcatctcggctgtcatctccttccc
gccactcatctccatagagaagaagggcgctggcggcgggcagcagccgg
ccgagccaagctgcaagatcaacgaccagaagtggtatgtcatctcctcg
tccatcggttccttcttcgcgccttgcctcatcatgatcctggtctacgt
gcgtatttaccagatcgccaagcgtcgcacccgcgtgcctcccagccgcc
ggggtccggacgcctgttccgcgccgccggggggcgccgatcgcaggccc
aacgggctgggcccggagcgcggcgcgggtcccacgggcgctgaggcgga
gccgctgcccacccagcttaacggtgccccgggggagcccgcgcccgccg
ggccccgcgatggggatgcgctggacctagaggagagttcgtcgtccgag
cacgccgagcggcccccggggccccgcagacccgaccgcggcccccgagc
caagggcaagacccgggcgagtcaggtgaagccgggggacagtctgccgc
ggcgcgggcccggggccgcggggccgggggcttcggggtccgggcacgga
gaggagcgcggcgggggcgccaaagcgtcgcgctggcgcgggaggcaaaa
ccgggagaaacgcttcacgttcgtgctggcggtggtgatcggcgtgttcg
tggtgtgttggtttccgttctttttcacctacacgctcatagcggtcggc
tgcccggtgcccagccagctcttcaacttcttcttctggttcggctactg
caacagctcgctgaaccctgttatctacaccatcttcaaccacgacttcc
gacgcgccttcaagaagatcctctgccgtggggacagaaaacgcatcgtg
tga


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