[Bioperl-l] FW: Help with hmmpfam
Kary Ann Del Carmen Soriano Ocana
Kary at ioc.fiocruz.br
Mon Apr 11 08:19:16 EDT 2005
Hi Marc:
When I run it via shell I do not have any problems, it runs perfectly (including this "print"), and it gives me the following result(1.-) eventually it creates de outputfile: searchio.out (2.- following).
In my mind, the problem is: php script is not recognizing this hmmpfam with system command.
Thank you very much.
Kary
1.- Result:
[kary at vivax MGE-Tryp_Mobile_Genetic_Elements_14_01_05]$ perl -w test_1_prueba_11_04.pl
aceita a descriço dos modulos
lee a base de dados
factory: Bio::Tools::Run::Hmmpfam=HASH(0x9ab0f38)search and run: Bio::SearchIO::hmmer=HASH(0x9acddac)
fin[kary at vivax MGE-Tryp_Mobile_Genetic_Elements_14_01_05]$ more searchio.out
tr|Q8GPE3 lEwFFhiGV0 -108 1.4e-05 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 Uge97N6Hov 1229 0.0e+00 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 5o31pMTfTD 358 2.9e-106 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 S9idxzhdAK 108 4.4e-31 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 eRcC2vN3jZ 67 1.1e-18 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 AEHBfMfmWH 154 6.6e-45 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 I6zf7ixS5D 1116 0.0e+00 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 bbHl2B5rlL 172 3.2e-50 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 G4UdcJgsXe 159 1.7e-46 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 U0RpshXJqE 304 6.4e-90 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 F7aL2AcPUu 96 2.2e-27 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 6dvvm1BKtB 114 9.0e-33 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 T3HBWp9YHA 555 1.1e-165 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 TPkc6EtVLN 151 7.3e-44 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 tQAf8GgYdG 50 1.2e-15 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 2kFyqaGTYl 37 1.3e-14 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 i6l3GMokJJ 114 1.2e-32 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 LMrNsiVENo 1135 0.0e+00 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 CfazgjGKUp 1128 0.0e+00 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 klmSPIXJ0B -3 3.5e-11 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 ViPul4YYKM 0 8.0e-10 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 t9vFE4UzS9 119 2.3e-34 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 As7DuhEAJB 4 2.0e-11 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 IG63mb6p4n 9 1.9e-10 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 3RnaG01Zyt 1147 0.0e+00 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 r6zA7KBX3Q 62 5.1e-17 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 ZpKGsPYYvP 240 1.0e-70 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 9HnSRY75Aa 30 1.3e-12 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 2a8vzyTUP1 166 2.5e-48 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 tBC6btpD1z 44 1.7e-12 Tnp-IS1191 - Streptococcus thermophilus.
tr|Q8GPE3 J3KfLxK6ot -3 2.7e-08 Tnp-IS1191 - Streptococcus thermophilus.
-----Original Message-----
From:
[mailto:Marc.Logghe at devgen.com]
Sent: Mon 4/11/2005 8:42 AM
To: Kary Ann Del Carmen Soriano Ocana; bioperl-l at portal.open-bio.org
Cc: Alberto M. R. Davila
Subject: RE: [Bioperl-l] FW: Help with hmmpfam
Hi Kary,
As far as I understood it correctly, you never get to the line 'print "search and run: $search\n";', meaning your perl script crashes earlier, when you envoke $factory->run.
Could you send the error message when you run the perl script from the command line, not via the php script ?
Cheers,
Marc
> Dear All,
> I need run a "php script" and call in it (with system
> command) other "script in perl/bioperl" for run hmmpfam. I
> would like (if possible) to obtain some help for execute this
> script, because recognize only perl script but at the moment
> of run hmmpfam (bioperl modules), it doesn't run it.
> I am listing my code below and the output containing the
> following error:
>
>
> (partial) output and error:
> aceita a descriço dos modulos
> lee a base de dados
> factory: Bio::Tools::Run::Hmmpfam=HASH(0x8be2d44)
>
> Última linha da saída: factory:
> Bio::Tools::Run::Hmmpfam=HASH(0x8be2d44) Valor de Retorno: 2
>
>
> I put some "print" commands everywhere to see where I am
> getting the error and looks like it is not entering/printing
> the while results (eg: factory, search). Any help would be
> greatly appreciated.
>
> Thanks, Kary
>
> ************
>
> Script:
>
> 1.- php:
> echo '<pre>';
>
> // Mostra todo o resultado do comando do shell 'perl', e
> retorna // a última linha da saída em $last_line. Guarda o
> valor de retorno // do comando shell em $retval.
> $last_line = system('/usr/bin/perl test_1.pl', $retval); //
> Mostrando informação adicional echo '
> </pre>
> <hr />Última linha da saída: '.$last_line.'
> <hr />Valor de Retorno: '.$retval
> 2.- perl:
> $ENV{HMMPFAMDIR} = '/usr/local/bin/hmmpfam'; use lib
> "/usr/local/bioperl14"; use lib "/usr/local/bioperl-run-1.4";
>
> use strict;
> use Bio::Tools::Run::Hmmpfam;
> use Bio::SearchIO;
> use Bio::SearchIO::Writer::HTMLResultWriter;
> use Bio::SearchIO::Writer::TextResultWriter;
> use Bio::SearchIO::Writer::HSPTableWriter;
> use Bio::SearchIO::Writer::ResultTableWriter;
> use Bio::SeqIO;
> print "aceita a descriço dos modulos\n"; my @params =
> ('DB' =>
> '/home/kary/public_html/MGE-Tryp_Mobile_Genetic_Elements_14_01
> _05/meus_modelos_hmms.hmm', 'E' => 0.0001);
> print "lee a base de dados\n";
> my $factory = Bio::Tools::Run::Hmmpfam->new(@params);
> print "factory: $factory";
> #any old protein fasta file
> my $search =
> $factory->run('/home/kary/public_html/MGE-Tryp_Mobile_Genetic_
> Elements_14_01_05/sequencia_fasta_1_tn.txt');
> print "search and run: $search\n";
> my $writer = Bio::SearchIO::Writer::HSPTableWriter->new(
> -columns => [qw(
> query_name
> hit_name
> score
> expect
> query_description
> )] ); my
> $out = Bio::SearchIO->new( -writer => $writer,
> -file => ">searchio.out" );
> while (my $result = $search->next_result()) {
> $out->write_result($result);
> }
> print "fin";
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l
>
>
More information about the Bioperl-l
mailing list