[Bio] / Sprout / SapServerTest4.pl Repository:
ViewVC logotype

Diff of /Sprout/SapServerTest4.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.1, Tue Mar 23 18:44:06 2010 UTC revision 1.7, Fri Nov 2 20:28:52 2012 UTC
# Line 3  Line 3 
3  use strict;  use strict;
4  use SeedEnv;  use SeedEnv;
5  use Tracer;  use Tracer;
6  use Data::Dumper;  use Sapling;
7  use gjoseqlib;  use ALITREserver;
 use find_special_proteins;  
   
 my $genome = $ARGV[0];  
 print "Reading contigs for $genome.\n";  
 my @contigs = gjoseqlib::read_fasta("$FIG_Config::organisms/$genome/contigs");  
 print "Connecting to server.\n";  
 my $anno = ANNOserver->new(url => 'http://bio-macpro-1.mcs.anl.gov/~parrello/FIG/anno_server.cgi');  
 print "Producing selenoprotein output.\n";  
 my $output = $anno->find_special_proteins({ -contigs => \@contigs });  
 my @list = @$output;  
 print "Producing pyrrolysine output.\n";  
 $output = $anno->find_special_proteins({ -contigs => \@contigs, -templates => 'pyrrolysine' });  
 push @list, @$output;  
 print "Results:\n" . Dumper(@list);  
8    
9        my ($sap, $sapObject, $altObject);
10        if ($ENV{SAS_SERVER} eq 'localhost') {
11            $sap = Sapling->new(dbName => 'pubseed_sapling_10', dbhost => 'localhost', port => 3399);
12    #        $sap = Sapling->new(dbName => 'pseed_sapling_07', dbhost => 'localhost', port => 3333);
13            $sapObject = SAPserver->new(sapDB => $sap, url => 'localhost');
14            $altObject = ALITREserver->new(sapDB => $sap, url => 'localhost');
15            $FIG_Config::orgCache = "P:/vol/public-pseed/SharedData/OrgCache";
16            $FIG_Config::attrHost = "localhost";
17            $FIG_Config::attrPort = 3333;
18        } else {
19            $sapObject = SAPserver->new();
20    #        $altObject = ALITREserver->new();
21        }
22    #
23    my @ids = qw( cfe6d12b8a842868ee25e4b775456cda
24                  03382fd0dbe13a282d4b7b01be7f9d9c
25                  616c2e7e50820a5862be6a2364206975
26                );
27    
28    my $result;
29    
30    $result = $sapObject->select( { -path   =>   'ProteinSequence',
31                               -filter => { 'ProteinSequence(id)' => \@ids },
32                               -fields => [ qw(id sequence) ],
33                             }
34                           );
35    
36    print Dumper( \@ids, $result );
37    
38    @ids = reverse @ids;
39    $result = $sapObject->select( { -path   =>   'ProteinSequence',
40                               -filter => { 'ProteinSequence(id)' => \@ids },
41                               -fields => [ qw(id sequence) ],
42                             }
43                           );
44    
45    print Dumper( \@ids, $result );
46  1;  1;

Legend:
Removed from v.1.1  
changed lines
  Added in v.1.7

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3