[Bio] / FigKernelScripts / p3-find-couples.pl Repository:
ViewVC logotype

Diff of /FigKernelScripts/p3-find-couples.pl

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

revision 1.2, Fri Aug 11 01:13:02 2017 UTC revision 1.3, Fri Dec 1 02:53:39 2017 UTC
# Line 12  Line 12 
12  if the category column contained roles, this program would output role couples. If the category column contained  if the category column contained roles, this program would output role couples. If the category column contained
13  global protein families, this program would output protein family couples.  global protein families, this program would output protein family couples.
14    
15    A blank value in the category column will cause the input line to be ignored.
16    
17  The output will be three columns-- the two category IDs and the number of times the couple occurred.  The output will be three columns-- the two category IDs and the number of times the couple occurred.
18    
19  =head2 Parameters  =head2 Parameters
# Line 112  Line 114 
114      for my $couplet (@$couplets) {      for my $couplet (@$couplets) {
115          my ($fid, $line) = @$couplet;          my ($fid, $line) = @$couplet;
116          my $category = $line->[$catCol];          my $category = $line->[$catCol];
117            if ($category) {
118          my ($start, $end, $sequence);          my ($start, $end, $sequence);
119          my $fidData = $rows{$fid};          my $fidData = $rows{$fid};
120          # Here we get the start and end.          # Here we get the start and end.
# Line 141  Line 144 
144          push @{$contigs{"$genomeID:$sequence"}}, [$category, $start, $end];          push @{$contigs{"$genomeID:$sequence"}}, [$category, $start, $end];
145      }      }
146  }  }
147    }
148  # Now we have category and position data for each feature sorted by sequence.  # Now we have category and position data for each feature sorted by sequence.
149  # For each list, we sort by start position and figure out what qualifies as a couple.  # For each list, we sort by start position and figure out what qualifies as a couple.
150  # The couples are counted in this hash, which is keyed by "element1\telement2".  # The couples are counted in this hash, which is keyed by "element1\telement2".

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

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3