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DEPENDENCIES  view on Meta::CPAN

| * Bio::Tools::Run::Alignment::MAFFT - Bio::Seq                               |
| * Bio::Tools::Run::Alignment::Muscle - Bio::Seq                              |
| * Bio::Tools::Run::Alignment::Probalign - Bio::Seq                           |
| * Bio::Tools::Run::Alignment::Probcons - Bio::Seq                            |
| * Bio::Tools::Run::Alignment::Proda - Bio::Seq                               |
| * Bio::Tools::Run::Alignment::StandAloneFasta - Bio::Seq                     |
 ==============================================================================
 ==============================================================================
| Distribution              | Module used - Description            | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| libwww-perl               | * HTTP::Request::Common - Functions  |   None    |
|                           |   that generate HTTP::Requests       |           |
|                           | * LWP - Libwww-perl                  |           |
|==============================================================================|
| Used by:                                                                     |
|------------------------------------------------------------------------------|
| * Bio::Installer::Generic - HTTP::Request::Common                            |
| * Bio::Installer::Generic - LWP                                              |
 ==============================================================================

lib/Bio/Tools/Run/Ensembl.pm  view on Meta::CPAN

    if ($use_swiss && (! $gene || @genes > 0)) {
        my $swiss_id;
        
        #*** swiss look up should be farmed out to some dedicated class
        my $swiss_name = lc($gene_name);
        my $swiss_species = lc($species);
        $swiss_species =~ s/\s/+/g;
        my $url = "http://www.expasy.org/cgi-bin/get-entries?db=sp&db=tr&DE=&GNc=AND&GN=$swiss_name&OC=$swiss_species&view=&num=100";
        my $web_agent = Bio::WebAgent->new();
        $web_agent->url($url);
        my $rq = HTTP::Request->new(GET=>$url);
        my $reply = $web_agent->request($rq);
        if ($reply->is_error) {
            $class->throw($reply->as_string()."\nError getting for url $url!\n");
        }
        my $content = $reply->content;
        if ($content && $content !~ /No entries have been found/) {
            my @possibles = split("<tr><td><input type=checkbox name=ac value=", $content);
            shift(@possibles);
            
            my @good_ids;