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

Paul Cantalupo pcantalupo at gmail.com
Thu Aug 18 08:55:18 EDT 2011


Punit

I think you want '$hit->description' not '$hsp->desc'

Paul

Paul Cantalupo
University of Pittsburgh





On Thu, Aug 18, 2011 at 8:14 AM, punit kumar <punit_vergoboy2004 at yahoo.co.in>
wrote:
> 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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