#!/opt/conda/conda-bld/meme_1618213960901/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehol/bin/perl

use strict;
use warnings;

=head1 NAME

rsat-retrieve-seq - Downloads the requested sequence from RSAT and writes it to standard out.

=head1 SYNOPSIS

rsat-retrieve-seq [options] <organism>

 Options: 
  -help               Display this help message.
  -server <WSDL URL>  Select the server.
  -start <pos>        Sequence read starting position relative to predicted TSS; default -1000
  -end <pos>          Sequence read end position relative to predicted TSS; default 200
 
 Reads the sequence specified from RSAT and writes it to standard out.

 Writes standard output.

=cut

use Data::Dumper;
use Getopt::Long;
use LWP::Simple;
use Pod::Usage;
use XML::Compile::SOAP11;
use XML::Compile::WSDL11;
use XML::Compile::Transport::SOAPHTTP;
use XML::LibXML;
use XML::LibXML::XPathContext;

sub main {
  my $help = 0; # FALSE
  my $server = 'http://pedagogix-tagc.univ-mrs.fr/rsat/web_services/RSATWS.wsdl';
  my $start = -1000;
  my $end = 200;
  GetOptions("help|?" => \$help, "server=s" => \$server, "start=i" => \$start, "end=i" => \$end) or pod2usage(2);
  pod2usage(0) if $help;
  my ($organism) = @ARGV;
  pod2usage(-msg => "Organism must be specified", -exitval => 2) unless defined $organism;
  pod2usage(-msg => "Start must be less than end", -exitval => 2) if $start > $end;

  #
  # output
  #     Return type.
  #     Accepted values: 'server' (result is stored on a file on the server),
  #     'client' (result is directly transferred to the client),
  #     'both' (result is stored on the server and transferred to the client), 
  #     and ticket (an identifier, allowing to monitor the job status and
  #     retrieve the result when it is done, is returned to the client).
  #     Default is 'both'.
  # organism
  #     Organism. Words need to be underscore separated (example: Escherichia_coli_K12).
  # query
  #     A list of query genes.
  # all
  #     Return sequences for all the genes of the organism if value = 1. Incompatible with query.
  # noorf
  #     Prevent overlap with upstream open reading frames (ORF) if value = 1.
  # from
  #     Inferior limit of the region to retrieve.
  #     Default is organism dependant (example: Saccharomyces cerevisiae = -800).
  # to
  #     Superior limit of the region to retrieve. Default is '-1'.
  # feattype
  #     Type of genome features to load. Supported: CDS, mRNA, tRNA, rRNA. 
  # type
  #     Sequence type. Supported: upstream, downstream, ORF (unspliced open reading frame).
  # format
  #     Sequence format. Supported: IG (Intelligenetics), WC (wconsensus), raw, FastA
  # lw
  #     Line width (0 for whole sequence on one line).
  # label
  #     Field(s) to be used in the sequence label. 
  #     Multiple fields can be specified, separated by commas. 
  #     Supported: id, name, organism_name, sequence_type, current_from, 
  #     current_to, ctg, orf_strand, reg_left, reg_right. 
  #     Default: name.
  # label_sep
  #     Separator between the label fields. Default: | (pipe character).
  # nocom
  #     No comments if value = 1. Only the identifier and the sequence are returned. 
  #     By default, the comment indicates the ORF and upstream sequence coordinates.
  # repeat
  #     Use the repeat masked version of the genome if value = 1.
  #     Warning: repeated regions are annotated for some genomes only.
  # imp_pos
  #     Admit imprecise positions if value = 1.
  #
  my %args = (
    'output' => 'server',
    'organism' => $organism,
    'all' => 1,
    'noorf' => 1,
    'from' => $start,
    'to' => $end,
    'feattype' => '',
    'type' => 'upstream',
    'format' => 'fasta',
    'lw' => 50,
    'label' => 'id,name',
    'label_sep' => '',
    'nocom' => 0,
    'repeat' => 0,
    'imp_pos' => 0
  );

  # Obtain the network address of the server from the WSDL document
  my $wsdl = XML::LibXML->new->parse_file($server);
  my $xpc = XML::LibXML::XPathContext->new($wsdl);
  $xpc->registerNs('wsdl', 'http://schemas.xmlsoap.org/wsdl/');
  $xpc->registerNs('soap', 'http://schemas.xmlsoap.org/wsdl/soap/');
  my $result = $xpc->findnodes('//wsdl:service/wsdl:port/soap:address/@location');
  if ($result->size != 1) {
    die("No server URL found in WSDL document");
  }
  my $net_address = $result->to_literal;
  # Trim the URL to the server 
  $net_address =~ s/\/web_services.*$//;

  # Request the sequence from the retreive_seq service
  # defined in the WSDL document.
  my $proxy = XML::Compile::WSDL11->new($wsdl);
  my $client = $proxy->compileClient('retrieve_seq');

  my $answer = $client->( request => {%args});

  if ( defined $answer ) {
    # The URL for the sequence file should be in the server field.
    if ($answer->{output}->{response}->{server}) {
      my $url = $answer->{output}->{response}->{server};
      # Replace the boilerplate at the start of the
      # URL with server network address
      $url =~ s/\$RSAT\/public_html/$net_address/;
      # Request the URL and stream to standardd out
      my $result = getprint($url);
      if ($result != 200) {
        die("HTTP response code: $result\n");
      }
      exit 0
    } else {
      print STDERR Dumper($answer);
      exit 1;
    }
  } else {
    die("No answer?!");
  }
}
main(); 1;
