Bio::Tools::Run::StandAloneBlastPlus HTML output

[bretonics]

How can we get an html output?

I have tried several things but it either outputs in html format (with errors) or regular format. This is how it looks:

No HTML Output

# Create StandAloneBlastPlus Factory
        my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
                    -db_data    => $subject,
                );

        # Perform BLAST call
        $fac->blastn(   -query          => $CRPfile,
                        -outfile        => $outFile,
                        -method_args    => [ -word_size => 7],
                    );

No HTML Output

# Create StandAloneBlastPlus Factory
        my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
                    -db_data    => $subject,
                );

        # Perform BLAST call
        $fac->blastn(   -query          => $CRPfile,
                        -outfile        => $outFile,
                        -method_args    => [ -word_size => 7, html => ''],
                    );

HTML Output, but no results stored in object when while ( my $result = $fac->next_result ) { ... }

# Create StandAloneBlastPlus Factory
        my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
                    -db_data    => $subject,
                );

        # Perform BLAST call
        $fac->blastn(   -query          => $CRPfile,
                        -outfile        => $outFile,
                        -method_args    => [ -word_size => 7, html => ' '],
                    );

[bosborne]

Andres,

It’s not clear what you are asking for. You’ve written that you can get HTML output, which is useful if you wanted to create Web pages, for example.

But then you’re attempting to parse HTML using SearchIO, and that won’t work, it’s not a supported format.

What is it that you are trying to do?

Brian O.

On Mar 16, 2017, at 3:17 PM, Andres Breton notifications@github.com wrote:

How can we get an html output?

I have tried several things but it either outputs in html format (with errors) or regular format. This is how it looks:

No HTML Output

Create StandAloneBlastPlus Factory

    my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
                -db_data    => $subject,
            );

    # Perform BLAST call
    $fac->blastn(   -query          => $CRPfile,
                    -outfile        => $outFile,
                    -method_args    => [ -word_size => 7],
                );

No HTML Output

Create StandAloneBlastPlus Factory

    my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
                -db_data    => $subject,
            );

    # Perform BLAST call
    $fac->blastn(   -query          => $CRPfile,
                    -outfile        => $outFile,
                    -method_args    => [ -word_size => 7, html => ''],
                );

HTML Output, but no results stored in object when while ( my $result = $fac->next_result ) { ... }

Create StandAloneBlastPlus Factory

    my $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
                -db_data    => $subject,
            );

    # Perform BLAST call
    $fac->blastn(   -query          => $CRPfile,
                    -outfile        => $outFile,
                    -method_args    => [ -word_size => 7, html => ' '],
                );

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/bioperl/bioperl-run/issues/48, or mute the thread https://github.com/notifications/unsubscribe-auth/AAQ99Jf-9Z9QVZ9oPTvLeGEKz74Ip4L0ks5rmYqugaJpZM4Mfwmq.

[bretonics]

Basically, what is the proper construction to call blastn on the factory object that will output the BLAST results as HTML rather than the default XML output?

Do you add it as a hash value in the method_args, and if so, how because it doesn't seem to work properly the way I did it.

[bosborne]

Your example works for me:

use Bio::Tools::Run::StandAloneBlastPlus;

Create StandAloneBlastPlus Factory

my $fac = Bio::Tools::Run::StandAloneBlastPlus->new( -db_data => 'test1.fa', );

Perform BLAST call

$fac->blastn( -query => 'test1.fa', -outfile => 'test.html', -method_args => [ -word_size => 7, html => '' ], );

However, as mentioned, you can not parse HTML output with SearchIO.

On Mar 20, 2017, at 9:47 AM, Andres Breton notifications@github.com wrote:

Basically, what is the proper construction to call blastn on the factory object that will output the BLAST results as HTML rather than the default XML output?

Do you add it as a hash value in the method_args, and if so, how because it doesn't seem to work properly the way I did it.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/bioperl/bioperl-run/issues/48#issuecomment-287763430, or mute the thread https://github.com/notifications/unsubscribe-auth/AAQ99GPMV-PPdKKoUdYVz9KSYHRr8EKkks5rnoNegaJpZM4Mfwmq.

[bretonics]

AH, I see what happens then. I thought I was calling the HTML output incorrectly somehow.

Thanks Brian.