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revision 1.1, Tue Mar 23 18:44:06 2010 UTC revision 1.3, Sat Oct 1 10:35:02 2011 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;  
8    
9  my $genome = $ARGV[0];      my ($sap, $sapObject, $altObject);
10  print "Reading contigs for $genome.\n";      if ($ENV{SAS_SERVER} eq 'localhost') {
11  my @contigs = gjoseqlib::read_fasta("$FIG_Config::organisms/$genome/contigs");          $sap = Sapling->new(dbName => 'pubseed_sapling_07', dbhost => 'localhost', port => 3399);
12  print "Connecting to server.\n";  #        $sap = Sapling->new(dbName => 'pseed_sapling_07', dbhost => 'localhost', port => 3333);
13  my $anno = ANNOserver->new(url => 'http://bio-macpro-1.mcs.anl.gov/~parrello/FIG/anno_server.cgi');          $sapObject = SAPserver->new(sapDB => $sap, url => 'localhost');
14  print "Producing selenoprotein output.\n";          $altObject = ALITREserver->new(sapDB => $sap, url => 'localhost');
15  my $output = $anno->find_special_proteins({ -contigs => \@contigs });          $FIG_Config::orgCache = "P:/vol/public-pseed/SharedData/OrgCache";
16  my @list = @$output;      } else {
17  print "Producing pyrrolysine output.\n";          $sapObject = SAPserver->new();
18  $output = $anno->find_special_proteins({ -contigs => \@contigs, -templates => 'pyrrolysine' });          $altObject = ALITREserver->new();
19  push @list, @$output;      }
20  print "Results:\n" . Dumper(@list);      my @complexes = qw(cpx00078 cpx00084 cpx00069);
21        my $retVal = $sapObject->complex_data(-ids => \@complexes,
22            -data => ['name', 'reactions', 'roles']);
23        print "All done.\n";
24    
25  1;  1;

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