Bio-Tools-Run-RemoteBlast

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META.json  view on Meta::CPAN

         }
      },
      "runtime" : {
         "requires" : {
            "Bio::Root::IO" : "0",
            "Bio::Root::Version" : "0",
            "Bio::SearchIO" : "0",
            "Bio::SeqIO" : "0",
            "Exporter" : "0",
            "Getopt::Long" : "0",
            "HTTP::Request::Common" : "0",
            "IO::String" : "0",
            "LWP" : "0",
            "base" : "0",
            "constant" : "0",
            "strict" : "0",
            "vars" : "0",
            "warnings" : "0"
         }
      },
      "test" : {

META.yml  view on Meta::CPAN

  url: http://module-build.sourceforge.net/META-spec-v1.4.html
  version: '1.4'
name: Bio-Tools-Run-RemoteBlast
requires:
  Bio::Root::IO: '0'
  Bio::Root::Version: '0'
  Bio::SearchIO: '0'
  Bio::SeqIO: '0'
  Exporter: '0'
  Getopt::Long: '0'
  HTTP::Request::Common: '0'
  IO::String: '0'
  LWP: '0'
  base: '0'
  constant: '0'
  strict: '0'
  vars: '0'
  warnings: '0'
resources:
  bugtracker: https://github.com/bioperl/bio-tools-run-remoteblast/issues
  homepage: https://metacpan.org/release/Bio-Tools-Run-RemoteBlast

Makefile.PL  view on Meta::CPAN

  "LICENSE" => "perl",
  "MIN_PERL_VERSION" => "5.006",
  "NAME" => "Bio::Tools::Run::RemoteBlast",
  "PREREQ_PM" => {
    "Bio::Root::IO" => 0,
    "Bio::Root::Version" => 0,
    "Bio::SearchIO" => 0,
    "Bio::SeqIO" => 0,
    "Exporter" => 0,
    "Getopt::Long" => 0,
    "HTTP::Request::Common" => 0,
    "IO::String" => 0,
    "LWP" => 0,
    "base" => 0,
    "constant" => 0,
    "strict" => 0,
    "vars" => 0,
    "warnings" => 0
  },
  "TEST_REQUIRES" => {
    "File::Spec" => 0,

Makefile.PL  view on Meta::CPAN

my %FallbackPrereqs = (
  "Bio::Root::IO" => 0,
  "Bio::Root::Version" => 0,
  "Bio::SearchIO" => 0,
  "Bio::SeqIO" => 0,
  "Exporter" => 0,
  "File::Spec" => 0,
  "Getopt::Long" => 0,
  "HTTP::Request::Common" => 0,
  "IO::Handle" => 0,
  "IO::String" => 0,
  "IPC::Open3" => 0,
  "LWP" => 0,
  "Test::More" => 0,
  "base" => 0,
  "constant" => 0,
  "strict" => 0,
  "vars" => 0,
  "warnings" => 0

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

package Bio::Tools::Run::RemoteBlast;
$Bio::Tools::Run::RemoteBlast::VERSION = '1.7.3';
use strict;
use warnings;

use Bio::SeqIO;
use IO::String;
use Bio::SearchIO;
use LWP;
use HTTP::Request::Common;
use Bio::Root::Version;

use constant {
    NOT_FINISHED => 0,
    ERR_QBSTATUS => 1,
    ERR_NOCONTENT => 2, 
    ERR_HTTPFAIL => 4,
    ERR_QBNONSPEC => 8
};
   

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

 Args    : Remote Blast ID (RID)

=cut

sub retrieve_blast {
    my($self, $rid) = @_;
    my $url_base = $self->get_url_base;
    my %hdr = %RETRIEVALHEADER;
    $hdr{'RID'} = $rid;
    
    my $req = HTTP::Request->new(
            GET => $url_base."?CMD=Get&FORMAT_OBJECT=SearchInfo&RID=$rid",
            );
    #$self->debug("SearchInfo request is " . $req->as_string());
    my $response = $self->ua->request($req);
    if( $response->is_success ) {
        my $status;
        if($response->content =~ /Status=(WAITING|ERROR|FAILED|UNKNOWN|READY)/i ) {
            $status = $1;
            if( $status eq 'ERROR' ) {
                $self->warn("Server Error");