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revision 1.5, Thu Oct 29 18:29:51 2009 UTC revision 1.7, Wed Feb 17 15:03:27 2010 UTC
# Line 11  Line 11 
11    
12  =head1 svr_upstream  =head1 svr_upstream
13    
14        svr_upstream <gene_ids.tbl >upstream_dna.fasta
15    
16  Retrieve upstream regions from the Sapling Server.  Retrieve upstream regions from the Sapling Server.
17    
18  This script takes as input a tab-delimited file with feature IDs at the end. For  This script takes as input a tab-delimited file with feature IDs at the end. For
# Line 50  Line 52 
52  if (! $opted) {  if (! $opted) {
53      print "usage: svr_upstream [--skipGene] [--size=200] [-url=http://...] <input >output\n";      print "usage: svr_upstream [--skipGene] [--size=200] [-url=http://...] <input >output\n";
54  } else {  } else {
55        # Fix STDIN.
56        ScriptThing::AdjustStdin();
57      # Get the server object.      # Get the server object.
58      my $sapServer = SAPserver->new(url => $url);      my $sapServer = SAPserver->new(url => $url);
59      # The main loop processes chunks of input, 1000 lines at a time.      # The main loop processes chunks of input, 1000 lines at a time.
# Line 59  Line 63 
63          # Ask the server for results.          # Ask the server for results.
64          my $document = $sapServer->upstream(-ids => [ map { $_->[0] } @tuples],          my $document = $sapServer->upstream(-ids => [ map { $_->[0] } @tuples],
65                                              -size => $size,                                              -size => $size,
66                                                -fasta => 1,
67                                              -comments => \%comments,                                              -comments => \%comments,
68                                              -skipGene => $skipGene);                                              -skipGene => $skipGene);
69          # Loop through the tuples, producing output.          # Loop through the tuples, producing output.

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