Bio-DB-NextProt

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lib/Bio/DB/NextProt.pm  view on Meta::CPAN

	my $self = {};
	$self->{_client}		= REST::Client->new({host=> "http://www.nextprot.org", timeout => 10,});
	$self->{_query}			= undef;
	$self->{_filter}		= undef;
	$self->{_chromosome}	= undef;
	$self->{_format}		= "json";
	bless($self, $class);
	return $self;
}

sub search_protein() {
	
	my $self  = shift;
    my %param = @_;

	my $path = "/rest/protein/list";

    $self->{_format} = $param{'-format'} if defined $param{'-format'};

	if (defined $param{'-query'} && defined $param{'-filter'}) {
		

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

		
		$self->{_client}->GET($path."?filter=".$param{'-filter'}."&format=".$self->{_format});
	}

	&reset_params();

	return $self->{_client}->responseContent();

}

sub search_cv() {
	my $self  = shift;
	my %param = @_;
	
	my $path   = "/rest/cv/list";

    $self->{_format} = $param{'-format'} if defined $param{'-format'};

    if (defined $param{'-query'} && defined $param{'-filter'}) {

        $self->{_client}->GET($path."?query=".$param{'-query'}."&filter=".$param{'-filter'}."&format=".$self->{_format});

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

        $self->{_client}->GET($path."?filter=".$param{'-filter'}."&format=".$self->{_format});
    }

	&reset_params();

	return $self->{_client}->responseContent();

}

sub get_protein_info() {
	my $self  = shift;
	my %param = @_;

	my $path   = "/rest/entry/";

    $self->{_format} = $param{'-format'} if defined $param{'-format'};

	if (defined $param{'-query'} && $param{'-retrieve'}) {

		$self->{_client}->GET($path.$param{'-query'}."/".$param{'-retrieve'}."?format=".$self->{_format});

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

		$self->{_client}->GET($path.$param{'-query'}."?format=".$self->{_format});
	}

	&reset_params();

	return $self->{_client}->responseContent();

}

sub get_isoform_info() {
	my $self  = shift;
	my %param = @_;

	my $path = "/rest/isoform/";

    $self->{_format} = $param{'-format'} if defined $param{'-format'};

    if (defined $param{'-query'} && $param{'-retrieve'}) {

        $self->{_client}->GET($path.$param{'-query'}."/".$param{'-retrieve'}."?format=".$self->{_format});

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

	    $self->{_client}->GET($path.$param{'-query'}."?format=".$self->{_format});
	}

	&reset_params();

	return $self->{_client}->responseContent();

}

sub get_protein_cv_info() {
	my $self  = shift;
	my %param = @_;

	my $path = "/rest/cv/";

	$self->{_format} = $param{'-format'} if defined $param{'-format'};

	if (defined $param{'-query'} && $param{'-retrieve'}) {
		
		$self->{_client}->GET($path.$param{'-query'}."/".$param{'-retrieve'}."?format=".$self->{_format});

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

        $self->{_client}->GET($path.$param{'-query'}."?format=".$self->{_format});
    }

	&reset_params();
    
	return $self->{_client}->responseContent();

}

sub get_accession_list() {
	my $self	= shift;
	my %param	= @_;

	my $path = "ftp://ftp.nextprot.org/pub/current_release/ac_lists";
	my @file = ();

	if ( defined $param{'-chromosome'} ) {

		$self->{_chromosome} = $param{'-chromosome'};
		my $chrom = $self->{_chromosome};

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

		} elsif ( $param{'-evidence'} eq "uncertain" ) {
			@file = ftp_get($path."/"."nextprot_ac_list_PE5_uncertain.txt")
		}
	}

	&reset_params();
	return @file;
}


sub get_hpp_report() {
	my $self	= shift;
	my %param	= @_;

	my $path = "ftp://ftp.nextprot.org/pub/current_release/custom/hpp";
	my @file = ();

	if ( defined $param{'-chromosome'} ) {

    	my $chrom = $param{'-chromosome'};
		@file = ftp_get($path."/"."HPP_chromosome_".$chrom.".txt");

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

	} elsif ( defined $param{'-nacetyl'} ) {
		@file = ftp_get($path."/"."HPP_entries_with_nacetyl_by_chromosome.txt");
	}

	&reset_params();
	return @file;
		
}


sub get_mapping() {
	my $self	= shift;
	my %param	= @_;

	my $path = "ftp://ftp.nextprot.org/pub/current_release/mapping";
	my @file = ();

	if ( defined $param{'-map'} ) {
		my $db = $param{'-map'};

		if ( $db eq 'ensembl_gene' ) {

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

		} elsif ( $db eq 'refseq' ) {
			@file = ftp_get($path."/"."nextprot_refseq.txt");
		}
	}
	
	&reset_params();
	return @file;

}

sub get_chromosome() {
	my $self  =	shift;
	my %param =	@_;

	my @data  = ();
	my %table = ();

	my $path = "ftp://ftp.nextprot.org/pub/current_release/chr_reports";

	if ( defined $param{'-chromosome'} ) {

lib/Bio/DB/NextProt.pm  view on Meta::CPAN

    for my $pair ( @data ) {
        
        chomp $pair;
        my ($key, $value) = split(/\t/, $pair);
        $map{$key} = $value;
    }

    return %map;
}

sub reset_params() {
	my $self = shift;

	$self->{_query}  = undef;
	$self->{_filter} = undef;
}

1;