BioPerl
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Bio/DB/BioFetch.pm view on Meta::CPAN
#
# Copyright Lincoln Stein
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
#
package Bio::DB::BioFetch;
use strict;
use HTTP::Request::Common 'POST';
=head1 NAME
Bio::DB::BioFetch - Database object interface to BioFetch retrieval
=head1 SYNOPSIS
use Bio::DB::BioFetch;
$bf = Bio::DB::BioFetch->new();
Bio/DB/BioFetch.pm view on Meta::CPAN
=cut
*get_Stream_by_batch = \&Bio::DB::WebDBSeqI::get_Stream_by_id;
=head1 The remainder of these methods are for internal use
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: returns a HTTP::Request object
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=cut
sub get_request {
my ($self, @qualifiers) = @_;
my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)],
@qualifiers);
Bio/DB/CUTG.pm view on Meta::CPAN
my $key = shift;
$key =~ s/^-//;
$self->$key(shift);
}
$self->url($URL);
###1st of all search DB to check species exists and is unique
my $nameparts = join "+", $self->sp =~ /(\S+)/g;
my $search_url =
$self->url . "/codon/cgi-bin/spsearch.cgi?species=" . $nameparts . "&c=s";
my $rq = HTTP::Request->new( GET => $search_url );
my $reply = $self->request($rq);
if ( $reply->is_error ) {
$self->throw(
$reply->as_string() . "\nError getting for url $search_url!\n" );
}
my $content = $reply->content;
return 0 unless $content;
$self->debug(" reply from query is \n $content");
##### if no matches, assign defaults - or can throw here? ######
if ( $content =~ /not found/i ) {
Bio/DB/CUTG.pm view on Meta::CPAN
$nameparts = $self->sp;
my $CT_url =
$self->url
. "/codon/cgi-bin/showcodon.cgi?species="
. $nameparts . "&aa="
. $self->gc
. "&style=GCG";
$self->debug("URL : $CT_url\n");
## retrieve data in html##
my $rq2 = HTTP::Request->new( GET => $CT_url );
$reply = $self->request($rq2);
if ( $reply->is_error ) {
$self->throw(
$reply->as_string() . "\nError getting for url $CT_url!\n" );
}
my $content2 = $reply->content;
## strip html tags, basic but works here
$content2 =~ s/<[^>]+>//sg;
$content2 =~ s/Format.*//sg;
Bio/DB/DBFetch.pm view on Meta::CPAN
=cut
# Let the code begin...
package Bio::DB::DBFetch;
use strict;
use vars qw($MODVERSION $DEFAULTFORMAT $DEFAULTLOCATION
$DEFAULTSERVERTYPE);
$MODVERSION = '0.1';
use HTTP::Request::Common;
use base qw(Bio::DB::WebDBSeqI);
# the new way to make modules a little more lightweight
BEGIN {
# global vars
$DEFAULTSERVERTYPE = 'dbfetch';
$DEFAULTLOCATION = 'ebi';
}
=head1 Routines from Bio::DB::WebDBSeqI
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: returns a HTTP::Request object
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=cut
sub get_request {
my ($self, @qualifiers) = @_;
my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)],
@qualifiers);
Bio/DB/EntrezGene.pm view on Meta::CPAN
Returns : A Bio::Seq object
Args : Gene id
Throws : "id does not exist" exception
=head1 Routines implemented by Bio::DB::NCBIHelper
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=head2 get_Stream_by_id
Title : get_Stream_by_id
Usage : $stream = $db->get_Stream_by_id( [$gid1, $gid2] );
Function: Gets a series of Seq objects using Gene ids
Returns : A Bio::SeqIO stream object
Args : A reference to an array of Gene ids
Bio/DB/GenBank.pm view on Meta::CPAN
Args : $ref : either an array reference, a filename, or a filehandle
from which to get the list of unique ids/accession numbers.
NOTE: This method is redundant and deprecated. Use get_Stream_by_id()
instead.
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=cut
=head2 default_format
Title : default_format
Usage : my $format = $self->default_format
Function: Returns default sequence format for this module
Bio/DB/GenPept.pm view on Meta::CPAN
Function: Gets a Seq objects by accession number
Returns : Bio::Seq object
Args : accession number to retrieve by
=head1 Routines implemented by Bio::DB::NCBIHelper
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=head2 get_Stream_by_id
Title : get_Stream_by_id
Usage : $stream = $db->get_Stream_by_id( [$uid1, $uid2] );
Function: Gets a series of Seq objects by unique identifiers
Returns : a Bio::SeqIO stream object
Args : $ref : a reference to an array of unique identifiers for
Bio/DB/GenericWebAgent.pm view on Meta::CPAN
if( defined $ua && $ua->isa("LWP::UserAgent") ) {
$self->{'_ua'} = $ua;
}
return $self->{'_ua'};
}
=head2 get_Response
Title : get_Response
Usage : $agent->get_Response;
Function: Get the HTTP::Response object by passing it an HTTP::Request (generated from
Bio::ParameterBaseI implementation).
Returns : HTTP::Response object or data if callback is used
Args : (optional)
-cache_response - flag to cache HTTP::Response object;
Default is 1 (TRUE, caching ON)
These are passed on to LWP::UserAgent::request() if stipulated
-cb - use a LWP::UserAgent-compliant callback
Bio/DB/HIV.pm view on Meta::CPAN
package Bio::DB::HIV;
use strict;
use warnings;
use vars qw( $LANL_BASE $LANL_MAP_DB $LANL_MAKE_SEARCH_IF $LANL_SEARCH );
# Object preamble - inherits from Bio::DB::WebDBSeqI
use Bio::Root::Root;
use HTTP::Request::Common;
use Bio::DB::HIV::HIVAnnotProcessor;
use base qw(Bio::DB::WebDBSeqI);
BEGIN {
# base change of 01/14/09
$LANL_BASE = "http://www.hiv.lanl.gov/components/sequence/HIV/asearch";
$LANL_MAP_DB = "map_db.comp";
$LANL_MAKE_SEARCH_IF = "make_search_if.comp";
Bio/DB/HIV.pm view on Meta::CPAN
return $self;
}
=head1 WebDBSeqI compliance
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: returns a HTTP::Request object
Returns :
Args : %qualifiers = a hash of qualifiers with keys in
(-ids, -format, -mode, -query)
Note : Several layers of requests are performed to get to the sequence;
see Bio::DB::Query::HIVQuery.
=cut
sub get_request {
my $self = shift;
Bio/DB/NCBIHelper.pm view on Meta::CPAN
preceded with a _
=cut
# Let the code begin...
package Bio::DB::NCBIHelper;
use strict;
use Bio::DB::Query::GenBank;
use HTTP::Request::Common;
use URI;
use Bio::Root::IO;
use Bio::DB::RefSeq;
use URI::Escape qw(uri_unescape);
use base qw(Bio::DB::WebDBSeqI Bio::Root::Root);
our $HOSTBASE = 'https://eutils.ncbi.nlm.nih.gov';
our $MAX_ENTRIES = 19000;
our $REQUEST_DELAY = 3;
Bio/DB/NCBIHelper.pm view on Meta::CPAN
=cut
sub default_format {
return $DEFAULTFORMAT;
}
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: HTTP::Request
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=cut
sub get_request {
my ( $self, @qualifiers ) = @_;
my ( $mode, $uids, $format, $query, $seq_start, $seq_stop, $strand,
$complexity )
= $self->_rearrange(
Bio/DB/Query/WebQuery.pm view on Meta::CPAN
preceded with a _
=cut
# Let the code begin...
package Bio::DB::Query::WebQuery;
use strict;
use URI;
use LWP::UserAgent;
use HTTP::Request::Common;
use base qw(Bio::Root::Root Bio::DB::QueryI);
=head2 new
Title : new
Usage : $db = Bio::DB::WebQuery->new(@args)
Function: create new query object
Returns : new query object
Args : -db database (e.g. 'protein')
Bio/DB/Query/WebQuery.pm view on Meta::CPAN
my $self = shift;
my $d = $self->{'_truncated'};
$self->{'_truncated'} = shift if @_;
$d;
}
=head2 _get_request
Title : _get_request
Usage : $http_request = $db->_get_request(@params)
Function: create an HTTP::Request with indicated parameters
Returns : HTTP::Request object
Args : CGI parameter list
=cut
sub _get_request {
my $self = shift;
my ($method,$base,@params) = $self->_request_parameters;
my $uri = URI->new($base);
my $request;
if ($method eq 'get') {
Bio/DB/SwissProt.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::DB::SwissProt;
use strict;
use HTTP::Request::Common;
our $MODVERSION = '0.8.1';
use base qw(Bio::DB::WebDBSeqI);
# global vars
our $DEFAULTSERVERTYPE = 'ebi';
our $DEFAULTFORMAT = 'swissprot';
# our $DEFAULTIDTRACKER = 'http://www.expasy.ch';
# you can add your own here theoretically.
Bio/DB/SwissProt.pm view on Meta::CPAN
};
=head2 Implemented Routines from Bio::DB::WebDBSeqI interface
=cut
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: returns a HTTP::Request object
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=cut
sub get_request {
my ($self, @qualifiers) = @_;
my ($uids, $format) = $self->_rearrange([qw(UIDS FORMAT)],
@qualifiers);
Bio/DB/SwissProt.pm view on Meta::CPAN
( 'format' => $f )
);
my $url = $self->location_url;
my $uid;
my $jointype = $HOSTS{$self->servertype}->{'jointype'} || ' ';
my $idvar = $HOSTS{$self->servertype}->{'idvar'} || 'id';
if( ref($uids) =~ /ARRAY/i ) {
# HTTP::Request automagically converts the ' ' to %20
$uid = join($jointype, @$uids);
} else {
$uid = $uids;
}
$vars{$idvar} = $uid;
return POST $url, \%vars;
}
=head2 postprocess_data
Bio/DB/WebDBSeqI.pm view on Meta::CPAN
my $seq = $db->get_Seq_by_id('ROA1_HUMAN')
=head1 DESCRIPTION
Provides core set of functionality for connecting to a web based
database for retrieving sequences.
Users wishing to add another Web Based Sequence Dabatase will need to
extend this class (see L<Bio::DB::SwissProt> or L<Bio::DB::NCBIHelper> for
examples) and implement the get_request method which returns a
HTTP::Request for the specified uids (accessions, ids, etc depending
on what query types the database accepts).
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the
evolution of this and other Bioperl modules. Send
your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation
Bio/DB/WebDBSeqI.pm view on Meta::CPAN
package Bio::DB::WebDBSeqI;
use strict;
use vars qw($MODVERSION %RETRIEVAL_TYPES $DEFAULT_RETRIEVAL_TYPE
$DEFAULTFORMAT $LAST_INVOCATION_TIME @ATTRIBUTES);
use Bio::SeqIO;
use Bio::Root::IO;
use LWP::UserAgent;
use POSIX 'setsid';
use HTTP::Request::Common;
use HTTP::Response;
use File::Spec;
use IO::Pipe;
use IO::String;
use Bio::Root::Root;
use base qw(Bio::DB::RandomAccessI);
BEGIN {
$MODVERSION = '0.8';
Bio/DB/WebDBSeqI.pm view on Meta::CPAN
$self->throw("accession.version does not exist") unless @seqs;
if( wantarray ) { return @seqs } else { return shift @seqs }
}
# implementing class must define these
=head2 get_request
Title : get_request
Usage : my $url = $self->get_request
Function: returns a HTTP::Request object
Returns :
Args : %qualifiers = a hash of qualifiers (ids, format, etc)
=cut
sub get_request {
my ($self) = @_;
my $msg = "Implementing class must define method get_request in class WebDBSeqI";
$self->throw($msg);
}
Bio/LiveSeq/IO/BioPerl.pm view on Meta::CPAN
A filename (or an ID that will fetch entry through the web) has to be passed
to this package which will return references to all translation objects
created from the EMBL entry. References to Transcription, DNA and Exon
objects can all be retrieved departing from these.
Alternatively, a specific "gene" name can be specified, together with
the embl-acc ID. This will create a LiveSeq::Gene object with all
relevant gene features attached/created.
ATTENTION: if web fetching is requested, the package HTTP::Request needs
to be installed.
=head1 AUTHOR - Joseph A.L. Insana
Email: Insana@ebi.ac.uk, jinsana@gmx.net
=head1 APPENDIX
The rest of the documentation details each of the object
Bio/LiveSeq/IO/BioPerl.pm view on Meta::CPAN
# why array from each_tag_value($qual) ? When will there be more than one
# element in such array?
# what is the annotation object? ($seqobj->annotation)
# unsatisfied by both BioPerl binomial and SRS "org" to retrieve Organism info
use strict;
use Carp qw(cluck croak carp);
use vars qw($DBEMBLLOADED);
use Bio::SeqIO; # for -file entry loading
# Note, the following requires HTTP::Request. If the modules are not installed
# uncomment the following and use only -filename and don't request swissprotinfo
eval {
require Bio::DB::EMBL; # for -id entry loading
$DBEMBLLOADED = 1;
};
use base qw(Bio::LiveSeq::IO::Loader);
# This package can in the future host other databases loading subroutines.
Bio/LiveSeq/IO/BioPerl.pm view on Meta::CPAN
if (defined($filename)) {
my $stream = Bio::SeqIO->new('-file' => $filename, '-format' => 'EMBL');
$seqobj = $stream->next_seq();
} else { # i.e. if -id
if( $DBEMBLLOADED ) {
my $embl = Bio::DB::EMBL->new();
$seqobj = $embl->get_Seq_by_id($id); # EMBL ID or ACC
} else {
my $root = Bio::Root::Root->new();
$root->warn("Must have HTTP::Request::Common installed, cannot run load without the -filename option specified, see docs for Bio::LiveSeq::IO::BioPerl");
return;
}
}
$hashref=&embl2hash($seqobj,\@embl_valid_feature_names,\@embl_valid_qual_names);
}
unless ($hashref) { return (0); }
%loader = (db => $db, filename => $filename, id => $id, hash => $hashref);
$obj = \%loader;
Bio/Perl.pm view on Meta::CPAN
my $genbank_db = undef;
my $genpept_db = undef;
my $embl_db = undef;
my $swiss_db = undef;
my $refseq_db = undef;
sub get_sequence{
my ($db_type,$identifier) = @_;
if( ! $DBOKAY ) {
confess ("Your system does not have one of LWP, HTTP::Request::Common, IO::String\n".
"installed so the DB retrieval method is not available.\n".
"Full error message is:\n $!\n");
return;
}
$db_type = lc($db_type);
my $db;
if( $db_type =~ /genbank/ ) {
if( !defined $genbank_db ) {
Bio/Tools/Analysis/DNA/ESEfinder.pm view on Meta::CPAN
# Let the code begin...
#should have own
package Bio::Tools::Analysis::DNA::ESEfinder;
use Data::Dumper;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw (POST);
use HTML::HeadParser;
use Bio::SeqFeature::Generic;
use Bio::Seq::Meta::Array;
use Bio::WebAgent;
use strict;
#inherits directly from SimpleAnalysisBase
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
Bio/Tools/Analysis/Protein/Domcut.pm view on Meta::CPAN
methods. Internal methods are usually preceded with a _
=cut
use strict;
package Bio::Tools::Analysis::Protein::Domcut;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw(GET);
use Bio::SeqFeature::Generic;
use Bio::Seq::Meta::Array;
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
my $URL = 'http://www.Bork.EMBL-Heidelberg.DE/Docu/mikita/domplot.cgi?';
my $ANALYSIS_NAME = 'Domcut';
my $ANALYSIS_SPEC =
{
'name' => 'Domcut',
Bio/Tools/Analysis/Protein/ELM.pm view on Meta::CPAN
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
use strict;
package Bio::Tools::Analysis::Protein::ELM;
use vars qw(%cc);
use HTML::HeadParser;
use Bio::SeqFeature::Generic;
use HTTP::Request::Common qw(POST);
use IO::String;
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
## valid cell compartments ##
%cc = (
all => 1,
nucleus => 'GO:0005634',
extracellular => 'GO:0005576',
cytoplasm => 'GO:0005737',
peroxisome => 'GO:0005777',
Bio/Tools/Analysis/Protein/ELM.pm view on Meta::CPAN
$self->warn(ref($self)." Request Error:\n".$r1->as_string);
return;
}
my $text = $r1->content;
my ($url) = $text =~ /URL=\S+(fun=\S+r=\d)/s;
#$url =~ s/amp;//g ;
my ($resp2);
$url = $URL . "?" .$url;
while (1) {
my $req2 = HTTP::Request->new(GET=>$url);
my $r2 = $self->request ($req2);
if ( $r2->is_error ) {
$self->warn(ref($self)." Request Error:\n".$r2->as_string);
return;
}
$resp2 = $r2->content();
if ($resp2 !~ /patient/s) {
$self->status('COMPLETED');
$resp2=~ s/<[^>]+>/ /sg;
Bio/Tools/Analysis/Protein/GOR4.pm view on Meta::CPAN
methods. Internal methods are usually preceded with a _
=cut
use strict;
package Bio::Tools::Analysis::Protein::GOR4;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw(POST);
use Bio::SeqFeature::Generic;
use Bio::Seq::Meta::Array;
$ENV{PERL_LWP_SSL_VERIFY_HOSTNAME} = 0;
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
use constant MIN_STRUC_LEN => 3;
my $URL = 'https://npsa-prabi.ibcp.fr/cgi-bin/secpred_sopma.pl';
my $ANALYSIS_NAME = 'GOR4';
my $ANALYSIS_SPEC = {name => 'Gor4', type => 'Protein'};
Bio/Tools/Analysis/Protein/GOR4.pm view on Meta::CPAN
notice => $self->seq->seq,
ali_width => 70,
];
my $content = $self->request($request);
my $text = $content->content;
return unless $text;
my ($next) = $text =~ /Prediction.*?=(.*?)>/;
return unless $next;
my $out = 'http://npsa-pbil.ibcp.fr/'.$next;
my $req2 = HTTP::Request->new(GET=>$out);
my $resp2 = $self->request($req2);
$self->status('COMPLETED') if $resp2 ne '';
$self->{'_result'} = $resp2->content;
}
1;
Bio/Tools/Analysis/Protein/HNN.pm view on Meta::CPAN
=cut
use strict;
package Bio::Tools::Analysis::Protein::HNN;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw (POST);
use Bio::SeqFeature::Generic;
use Bio::Seq::Meta::Array;
$ENV{PERL_LWP_SSL_VERIFY_HOSTNAME} = 0;
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
#extends array for 2struc.
my $URL = 'http://npsa-pbil.ibcp.fr/cgi-bin/secpred_hnn.pl';
my $ANALYSIS_NAME= 'HNN';
Bio/Tools/Analysis/Protein/HNN.pm view on Meta::CPAN
title => "",
notice => $self->seq->seq,
ali_width => 70,
];
my $text = $self->request($request)->content;
return unless $text;
my ($next) = $text =~ /Prediction.*?=(.*?)>/;
return unless $next;
my $out = "http://npsa-pbil.ibcp.fr/".$next;
my $req2 = HTTP::Request->new(GET=>$out);
my $resp2 = $self->request ($req2);
$self->status('COMPLETED') if $resp2 ne '';
$self->{'_result'} = $resp2->content;
return $self;
}
=head2 result
NAme : result
Bio/Tools/Analysis/Protein/NetPhos.pm view on Meta::CPAN
# Let the code begin...
package Bio::Tools::Analysis::Protein::NetPhos;
use vars qw($FLOAT);
use strict;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw (POST);
use Bio::SeqFeature::Generic;
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
$FLOAT = '[+-]?\d*\.\d*';
my $URL = 'http://www.cbs.dtu.dk/cgi-bin/nph-webface';
my $ANALYSIS_SPEC =
{
Bio/Tools/Analysis/Protein/Scansite.pm view on Meta::CPAN
# Let the code begin...
package Bio::Tools::Analysis::Protein::Scansite;
use vars qw($FLOAT @STRINGENCY);
use strict;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw(POST);
use Bio::SeqFeature::Generic;
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
$FLOAT = '[+-]?\d*\.\d*';
@STRINGENCY = qw(High Medium Low);
my $URL = 'http://scansite.mit.edu/cgi-bin/motifscan_seq';
my $ANALYSIS_SPEC =
Bio/Tools/Analysis/Protein/Sopma.pm view on Meta::CPAN
=head1 APPENDIX
=cut
use strict;
package Bio::Tools::Analysis::Protein::Sopma;
use IO::String;
use Bio::SeqIO;
use HTTP::Request::Common qw (POST);
use Bio::SeqFeature::Generic;
use Bio::Seq::Meta::Array;
$ENV{PERL_LWP_SSL_VERIFY_HOSTNAME} = 0;
use base qw(Bio::Tools::Analysis::SimpleAnalysisBase);
#extends array for 2struc.
my $URL = 'https://npsa-prabi.ibcp.fr/cgi-bin/secpred_sopma.pl';
my $ANALYSIS_NAME= 'Sopma';
my $ANALYSIS_SPEC= {name => 'Sopma', type => 'Protein'};
Bio/Tools/Analysis/Protein/Sopma.pm view on Meta::CPAN
width => $self->window_width,
];
my $text = $self->request($request)->content;
return $self unless $text;
#### get text only version of results ##
my ($next) = $text =~ /Prediction.*?=(.*?)>/;
return $self unless $next;
my $out = "http://npsa-pbil.ibcp.fr/". "$next";
my $req2 = HTTP::Request->new(GET=>$out);
my $resp2 = $self->request ($req2);
$self->{'_result'} = $resp2->content;
$self->status('COMPLETED') if $resp2 ne '';
return $self;
}
sub _add_params_to_result{
## called when making Seqfeature objects
my ($self, $tag_hash) = @_;
my $hash;
Bio/Tools/Run/RemoteBlast.pm view on Meta::CPAN
package Bio::Tools::Run::RemoteBlast;
use strict;
use warnings;
use Bio::SeqIO;
use IO::String;
use Bio::SearchIO;
use LWP;
use HTTP::Request::Common;
use Bio::Root::Version;
use constant {
NOT_FINISHED => 0,
ERR_QBSTATUS => 1,
ERR_NOCONTENT => 2,
ERR_HTTPFAIL => 4,
ERR_QBNONSPEC => 8
};
Bio/Tools/Run/RemoteBlast.pm view on Meta::CPAN
Args : Remote Blast ID (RID)
=cut
sub retrieve_blast {
my($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");
[ 0, 'Remote analysis POST submissions/Bio::SearchIO::blastxml' ],
'HTML::HeadParser' => [
3,
'Parsing <HEAD> section of HTML docs/Bio::Tools::Analysis::DNA::ESEfinder'
],
'HTML::TableExtract' =>
[ 0, 'Parsing HTML tables/Bio::DB::SeqVersion::gi' ],
'HTTP::Request::Common' => [
0,
'GenBank+GenPept sequence retrieval, remote http Blast jobs'
. '/Bio::DB::*,Bio::Tools::Run::RemoteBlast,'
. 'Bio::Tools::Analysis::Protein*,Bio::Tools::Analysis::DNA*'
],
'Inline::C' => [ 0.67, 'Speeding up code like Fasta Bio::DB::Fasta' ],
'IO::Scalar' => [
0, 'Deal with non-seekable filehandles/Bio::Tools::GuessSeqFormat'
DEPENDENCIES view on Meta::CPAN
|---------------------------+--------------------------------------+-----------|
| HTML-TableExtract | * HTML::TableExtract - NA | None |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::DB::SeqVersion::gi - HTML::TableExtract |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| HTTP-Message | * HTTP::Request::Common - NA | None |
| | * HTTP::Response - NA | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
| * Bio::DB::DBFetch - HTTP::Request::Common |
| * Bio::DB::HIV - HTTP::Request::Common |
| * Bio::DB::NCBIHelper - HTTP::Request::Common |
| * Bio::DB::SwissProt - HTTP::Request::Common |
| * Bio::DB::WebDBSeqI - HTTP::Request::Common |
| * Bio::DB::Query::WebQuery - HTTP::Request::Common |
| * Bio::Tools::Run::RemoteBlast - HTTP::Request::Common |
| * Bio::DB::WebDBSeqI - HTTP::Response |
==============================================================================
==============================================================================
| Distribution | Module used - Description | Min. ver. |
|---------------------------+--------------------------------------+-----------|
| IO-Compress | * Compress::Zlib - NA | None |
| | * IO::Uncompress::Gunzip - NA | |
|==============================================================================|
| Used by: |
|------------------------------------------------------------------------------|
"Clone" : "0",
"Convert::Binary::C" : "0",
"DB_File" : "0",
"Error" : "0",
"GD" : "0",
"Graph" : "0.5",
"GraphViz" : "0",
"HTML::Entities" : "0",
"HTML::HeadParser" : "3",
"HTML::TableExtract" : "0",
"HTTP::Request::Common" : "0",
"IO::Scalar" : "0",
"Inline::C" : "0.67",
"LWP::UserAgent" : "0",
"List::MoreUtils" : "0",
"PostScript::TextBlock" : "0",
"SVG" : "2.26",
"SVG::Graph" : "0.01",
"Set::Scalar" : "0",
"Sort::Naturally" : "0",
"Spreadsheet::ParseExcel" : "0",
Clone: '0'
Convert::Binary::C: '0'
DB_File: '0'
Error: '0'
GD: '0'
Graph: '0.5'
GraphViz: '0'
HTML::Entities: '0'
HTML::HeadParser: '3'
HTML::TableExtract: '0'
HTTP::Request::Common: '0'
IO::Scalar: '0'
Inline::C: '0.67'
LWP::UserAgent: '0'
List::MoreUtils: '0'
PostScript::TextBlock: '0'
SVG: '2.26'
SVG::Graph: '0.01'
Set::Scalar: '0'
Sort::Naturally: '0'
Spreadsheet::ParseExcel: '0'
scripts/Bio-DB-GFF/bp_genbank2gff3.pl view on Meta::CPAN
$source_type ||= "region"; # should really parse from FT.source contents below
#my $FTSOmap = $tm->FT_SO_map();
my $FTSOmap;
my $FTSOsynonyms;
if (defined($SO_FILE) && $SO_FILE eq 'live') {
print "\nDownloading the latest SO file from ".SO_URL."\n\n";
use LWP::UserAgent;
my $ua = LWP::UserAgent->new(timeout => 30);
my $request = HTTP::Request->new(GET => SO_URL);
my $response = $ua->request($request);
if ($response->status_line =~ /200/) {
use File::Temp qw/ tempfile /;
my ($fh, $fn) = tempfile();
print $fh $response->content;
$SO_FILE = $fn;
} else {
print "Couldn't download SO file online...skipping validation.\n"
scripts/DB/bp_biofetch_genbank_proxy.pl view on Meta::CPAN
#!perl
# dbfetch style caching proxy for GenBank
use strict;
use warnings;
use CGI qw(:standard);
use HTTP::Request::Common;
use LWP::UserAgent;
use Cache::FileCache;
use vars qw(%GOT $BUFFER %MAPPING $CACHE);
use constant CACHE_LOCATION => '/usr/tmp/dbfetch_cache';
use constant MAX_SIZE => 100_000_000; # 100 megs, roughly
use constant CACHE_DEPTH => 4;
use constant EXPIRATION => "1 week";
use constant PURGE => "1 hour";
t/LocalDB/Registry.t view on Meta::CPAN
-format => 'fasta',
-index => 'bdb',
-write_flag => 1 );
ok defined($bdb);
$entries = $bdb->build_index(test_input_file('cysprot.fa'));
is $entries, 7;
}
SKIP: {
test_skip(-tests => 9,
-requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)],
-requires_networking => 1);
my $registry = Bio::DB::Registry->new();
ok defined($registry);
my @available_services = $registry->services;
ok grep /testflat/,@available_services;
my $db = $registry->get_database('testflat');
ok defined($db);
my $seq = $db->get_Seq_by_id("ALEU_HORVU");
( run in 1.357 second using v1.01-cache-2.11-cpan-de7293f3b23 )