[Bioperl-l] query about Bio::Tools::Run::RemoteBlast

punit kumar punit_vergoboy2004 at yahoo.co.in
Thu Aug 18 08:14:54 EDT 2011


hi friends , 

i am new to Bioperl , and i am using "Bio::Tools::Run::RemoteBlast" for remote blast  i tried to use this module and i succeed a little yet, i want to get the description part of blast alignments which were found against my query sequence, as result is shown in format as given below, which is the out put table of ONLINE BLAST,

Sequences producing significant alignments:
Accession
Description
Max score
Total score
Query coverage
E value
Links
NP_216760.1 acyl carrier protein [Mycobacterium tuberculosis H37Rv] >ref|NP_336774.1| acyl carrier protein [Mycobacterium tuberculosis CDC1551] >ref|NP_855917.1| acyl carrier protein [Mycobacterium bovis AF2122/97] >ref|YP_978350.1| acyl carrier protein [Mycobacterium bovis BCG str. Pasteur 1173P2] >ref|YP_001283588.1| acyl carrier protein [Mycobacterium tuberculosis H37Ra] >ref|YP_001288206.1| acyl carrier protein [Mycobacterium tuberculosis F11] >ref|ZP_02551632.1| acyl carrier protein [Mycobacterium tuberculosis H37Ra] >ref|YP_002645307.1| acyl carrier protein [Mycobacterium bovis BCG str. Tokyo 172] >ref|YP_003031689.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis KZN 1435] >ref|ZP_04925721.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis C] >ref|ZP_04981085.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis str. Haarlem] >ref|ZP_05141736.1| acyl carrier
 protein [Mycobacterium tuberculosis '98-R604 INH-RIF-EM'] >ref|ZP_06433498.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis T46] >ref|ZP_06437620.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis CPHL_A] >ref|ZP_06443178.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis KZN 605] >ref|ZP_06450592.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis T17] >ref|ZP_06455160.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis K85] >ref|ZP_06504896.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis 02_1987] >ref|ZP_06510220.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis T92] >ref|ZP_06513730.1| meromycolate extension acyl carrier protein acpm [Mycobacterium tuberculosis EAS054] >ref|ZP_06517747.1| meromycolate extension acyl carrier protein acpm
 [Mycobacterium tuberculosis T85] >ref|ZP_06521786.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis GM 1503] >ref|ZP_06799170.1| acyl carrier protein [Mycobacterium tuberculosis 210] >ref|ZP_06952619.1| acyl carrier protein [Mycobacterium tuberculosis KZN 4207] >ref|ZP_06960948.1| acyl carrier protein [Mycobacterium tuberculosis KZN R506] >ref|ZP_07013145.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis 94_M4241A] >ref|ZP_07414839.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu001] >ref|ZP_07418616.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu002] >ref|ZP_07423348.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu003] >ref|ZP_07427715.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu004] >ref|ZP_07432018.1| meromycolate extension acyl carrier protein
 acpM [Mycobacterium tuberculosis SUMu005] >ref|ZP_07436410.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu006] >ref|ZP_07440655.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu008] >ref|ZP_07445228.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu007] >ref|ZP_07481045.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu009] >ref|ZP_07485275.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu010] >ref|ZP_07489492.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu011] >ref|ZP_07494023.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu012] >ref|ZP_07816044.1| acyl carrier protein [Mycobacterium tuberculosis KZN V2475] >ref|YP_004723912.1| meromycolate extension acyl carrier protein ACPM [Mycobacterium africanum
 GM041182] >ref|YP_004745700.1| meromycolate extension acyl carrier protein ACPM [Mycobacterium canettii CIPT 140010059] >sp|P0A4W6.1|ACPM_MYCTU RecName: Full=Meromycolate extension acyl carrier protein; Short=ACP >sp|P0A4W7.1|ACPM_MYCBO RecName: Full=Meromycolate extension acyl carrier protein; Short=ACP >emb|CAA94640.1| MEROMYCOLATE EXTENSION ACYL CARRIER PROTEIN ACPM [Mycobacterium tuberculosis H37Rv] >gb|AAK46588.1| acyl carrier protein [Mycobacterium tuberculosis CDC1551] >emb|CAD97121.1| MEROMYCOLATE EXTENSION ACYL CARRIER PROTEIN ACPM [Mycobacterium bovis AF2122/97] >emb|CAL72249.1| Meromycolate extension acyl carrier protein acpM [Mycobacterium bovis BCG str. Pasteur 1173P2] >gb|EAY60463.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis C] >gb|EBA42598.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis str. Haarlem] >gb|ABQ74026.1| meromycolate extension acyl carrier protein AcpM
 [Mycobacterium tuberculosis H37Ra] >gb|ABR06604.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis F11] >dbj|BAH26539.1| acyl carrier protein [Mycobacterium bovis BCG str. Tokyo 172] >gb|ACT24794.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis KZN 1435] >gb|EFD13913.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis T46] >gb|EFD18035.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis CPHL_A] >gb|EFD21093.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis KZN 605] >gb|EFD43942.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis K85] >gb|EFD47767.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis T17] >gb|EFD53534.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis 02_1987] >gb|EFD58858.1| meromycolate extension acyl carrier
 protein acpM [Mycobacterium tuberculosis T92] >gb|EFD62368.1| meromycolate extension acyl carrier protein acpm [Mycobacterium tuberculosis EAS054] >gb|EFD73930.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis GM 1503] >gb|EFD77945.1| meromycolate extension acyl carrier protein acpm [Mycobacterium tuberculosis T85] >gb|EFI30824.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis 94_M4241A] >gb|EFO74536.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu001] >gb|EFP15742.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu002] >gb|EFP19094.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu003] >gb|EFP22930.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu004] >gb|EFP26734.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu005]
 >gb|EFP30496.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu006] >gb|EFP33906.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu007] >gb|EFP38213.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu008] >gb|EFP42922.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu009] >gb|EFP46864.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu010] >gb|EFP50800.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu011] >gb|EFP54373.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis SUMu012] >gb|EGB28294.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis CDC1551A] >gb|EGE50793.1| meromycolate extension acyl carrier protein acpM [Mycobacterium tuberculosis W-148] >gb|AEB03875.1| meromycolate extension acyl
 carrier protein acpM [Mycobacterium tuberculosis KZN 4207] >gb|AEJ47271.1| acyl carrier protein [Mycobacterium tuberculosis CCDC5079] >gb|AEJ50890.1| acyl carrier protein [Mycobacterium tuberculosis CCDC5180] >emb|CCC27325.1| meromycolate extension acyl carrier protein ACPM [Mycobacterium africanum GM041182] >emb|CCC44598.1| meromycolate extension acyl carrier protein ACPM [Mycobacterium canettii CIPT 140010059] >emb|CCC64838.1| Meromycolate extension acyl carrier protein acpM [Mycobacterium bovis BCG str. Moreau RDJ] 223 223 100% 1e-74  
1KLP_A Chain A, The Solution Structure Of Acyl Carrier Protein From Mycobacterium Tuberculosis 220 220 99% 2e-73  
ZP_04748738.1 acyl carrier protein [Mycobacterium kansasii ATCC 12478] 165 165 100% 9e-52  
ZP_05224070.1 acyl carrier protein [Mycobacterium intracellulare ATCC 13950] 162 162 100% 8e-51  
NP_960931.1 acyl carrier protein [Mycobacterium avium subsp. paratuberculosis K-10] >ref|YP_881402.1| acyl carrier protein [Mycobacterium avium 104] >ref|ZP_05216419.1| acyl carrier protein [Mycobacterium avium subsp. avium ATCC 25291] >gb|AAS04314.1| AcpM [Mycobacterium avium subsp. paratuberculosis K-10] >gb|ABK65172.1| acyl carrier protein [Mycobacterium avium 104] >gb|EGO40713.1| acyl carrier protein [Mycobacterium avium subsp. paratuberculosis S397] 162 162 100% 8e-51  
NP_302135.1 acyl carrier protein [Mycobacterium leprae TN] >ref|YP_002503765.1| acyl carrier protein [Mycobacterium leprae Br4923] >sp|O69475.1|ACPM_MYCLE RecName: Full=Meromycolate extension acyl carrier protein; Short=ACP >emb|CAA19202.1| acyl carrier protein [Mycobacterium leprae] >emb|CAC30605.1| acyl carrier protein (meromycolate extension) [Mycobacterium leprae] >emb|CAR71749.1| acyl carrier protein (meromycolate extension) [Mycobacterium leprae Br4923] 162 162 100% 2e-50  
ZP_07966703.1 hypothetical protein HMPREF9336_03075 [Segniliparus rugosus ATCC BAA-974] >gb|EFV12044.1| hypothetical protein HMPREF9336_03075 [Segniliparus rugosus ATCC BAA-974] 162 162 88% 3e-50  
YP_905336.1 acyl carrier protein [Mycobacterium ulcerans Agy99] >ref|YP_001851618.1| meromycolate extension acyl carrier protein AcpM [Mycobacterium marinum M] >gb|ABL03865.1| meromycolate extension acyl carrier protein AcpM [Mycobacterium ulcerans Agy99] >gb|ACC41763.1| meromycolate extension acyl carrier protein AcpM [Mycobacterium marinum M] 161 161 100% 3e-50  
ZP_08713925.1 acyl carrier protein [Mycobacterium colombiense CECT 3035] >gb|EGT87768.1| acyl carrier protein [Mycobacterium colombiense CECT 3035] 160 160 100% 6e-50  
YP_003660002.1 phosphopantetheine-binding protein [Segniliparus rotundus DSM 44985] >gb|ADG99171.1| phosphopantetheine-binding protein [Segniliparus rotundus DSM 44985] 160 160 88% 8e-50  

                      where in my code:

print "hit name is ",$hit->name, "\n"; # gives me the refrence of aligned sequence
      print"Score: ".$hsp->score."\n";  # gives me the score of aligned sequence
      print"E-val: ".$hsp->expect."\n";  # gives me the evalue of aligned sequence
      print"percent identity: ".$hsp->percent_identity."\n";  # gives me the query coverage  of aligned sequence

i want to use  #print "Description ",$hsp->desc, "\n"; to show the description but i am not getting can any body help me out for this i need to know urgently, thanks to read and i hope i was succesfull to explain my problem .

below is the copy of my code i am trying to use :




  use Bio::Tools::Run::RemoteBlast;
  use strict;
  my $v = 1;
  my $prog = 'blastp';
  my $db   = 'refseq_protein';
  my $e_val= '1e-10'; #1e-10

 my $result;
 #my $code=q| my $answer = my $a / my $b;|;



   

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

  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
  $v = 1;
  my $str = Bio::SeqIO->new(-file=>'prot.txt' , '-format' => 'fasta' );
  my $input;
  while($input = $str->next_seq())
  {
  
  #  Blast a sequence against a database:
  
  my $r = $factory->submit_blast($input);
  print STDERR "waiting..." if( $v > 0 );
  
  my %hit_evalue;
  my @evalue;
  
  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 { 
        $factory->remove_rid($rid);
        #print $rid."\n\n";
      my $result = $rc->next_result;
      
        print "db is ", $result->database_name(), "\n";
        my $count = 0;
        while( my $hit = $result->next_hit ) {
    $count++;
    #next unless ( $v > 0);
    #print "hit name is ", $hit->name, "\n";
    while( my $hsp = $hit->next_hsp )
  {
      print "hit name is ",$hit->name, "\n";
      #print "Query name is ",$hsp->desc, "\n"; exit;
      
      print"Score: ".$hsp->score."\n";
      print"E-val: ".$hsp->expect."\n";
      print"percent identity: ".$hsp->percent_identity."\n";
    }
  
  
        }
    }
      }
  }
  }


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