[Bio] / FigKernelScripts / build_solid_set.pl Repository:
ViewVC logotype

Diff of /FigKernelScripts/build_solid_set.pl

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

revision 1.2, Wed Jan 16 16:37:49 2013 UTC revision 1.3, Fri Feb 1 16:49:36 2013 UTC
# Line 3  Line 3 
3  use Carp;  use Carp;
4  use SeedUtils;  use SeedUtils;
5  use GenerateClusters;  use GenerateClusters;
6    use FIG;
7  #  my $fig = new FIG;
 # This is a SAS Component  
 #  
   
8    
9  =head1 svr_build_solid_set -g CloseGenomes < clustersRel  =head1 svr_build_solid_set -g CloseGenomes < clustersRel
10    
# Line 67  Line 64 
64          push(@$set,$2);          push(@$set,$2);
65          $last = <STDIN>;          $last = <STDIN>;
66      }      }
67        if ($set = &ok_set($set,$fig))
68        {
69      push(@sets,$set);      push(@sets,$set);
70  }  }
71    }
72  print STDERR scalar @sets, " sets were read\n";  print STDERR scalar @sets, " sets were read\n";
73  my $ref = &SeedUtils::genome_of($sets[0]->[0]);  my $ref = &SeedUtils::genome_of($sets[0]->[0]);
74  print STDERR "reference genome = $ref\n";  print STDERR "reference genome = $ref\n";
# Line 89  Line 89 
89      print "//\n";      print "//\n";
90  }  }
91    
92    sub ok_set {
93        my($set,$fig) = @_;
94    
95        my @ok_pegs = grep { my $f = $fig->function_of($_); $f !~ /transport|regulat/ } @$set;
96        if     (@ok_pegs >= (0.5 * @$set))  { return $set }
97        elsif  (@ok_pegs > 2)               { return \@ok_pegs }
98        else                                { return undef }
99    }
100    
101    
102  sub project {  sub project {
103      my($set,$ref,$g,$corrH,$sapO) = @_;      my($set,$ref,$g,$corrH,$sapO) = @_;
104    

Legend:
Removed from v.1.2  
changed lines
  Added in v.1.3

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3