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Top Forums Shell Programming and Scripting awk? adjacency matrix to adjacency list / correlation matrix to list Post 302560866 by durden_tyler on Sunday 2nd of October 2011 01:27:44 AM
Old 10-02-2011
Using Perl on a space-delimited file:

Code:
$
$
$ cat f11
        AA      AB      AC      BB      ZZ
AA      1       0       0.5     0       0.7
AB      0       1       0.3     0       0
AC      0       0       1       0       0.1
BB      0       0       0       1       0
ZZ      0       0       0       0       1
$
$
$ perl -lane 'if ($.==1){@x=@F} else {for($i=1; $i<=$#F; $i++){print "$F[0] (gg) $x[$i-1] = $F[$i]" if $F[$i] != 0}}' f11
AA (gg) AA = 1
AA (gg) AC = 0.5
AA (gg) ZZ = 0.7
AB (gg) AB = 1
AB (gg) AC = 0.3
AC (gg) AC = 1
AC (gg) ZZ = 0.1
BB (gg) BB = 1
ZZ (gg) ZZ = 1
$
$

tyler_durden
This User Gave Thanks to durden_tyler For This Post:
 

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Graph::AdjacencyMatrix(3pm)				User Contributed Perl Documentation			       Graph::AdjacencyMatrix(3pm)

NAME
Graph::AdjacencyMatrix - create and query the adjacency matrix of graph G SYNOPSIS
use Graph::AdjacencyMatrix; use Graph::Directed; # or Undirected my $g = Graph::Directed->new; $g->add_...(); # build $g my $am = Graph::AdjacencyMatrix->new($g); $am->is_adjacent($u, $v) my $am = Graph::AdjacencyMatrix->new($g, distance_matrix => 1); $am->distance($u, $v) my $am = Graph::AdjacencyMatrix->new($g, attribute_name => 'length'); $am->distance($u, $v) my $am = Graph::AdjacencyMatrix->new($g, ...); my @V = $am->vertices(); DESCRIPTION
You can use "Graph::AdjacencyMatrix" to compute the adjacency matrix and optionally also the distance matrix of a graph, and after that query the adjacencyness between vertices by using the "is_adjacent()" method, or query the distance between vertices by using the "distance()" method. By default the edge attribute used for distance is "w", but you can change that in new(), see below. If you modify the graph after creating the adjacency matrix of it, the adjacency matrix and the distance matrix may become invalid. Methods Class Methods new($g) Construct the adjacency matrix of the graph $g. new($g, options) Construct the adjacency matrix of the graph $g with options as a hash. The known options are distance_matrix => boolean By default only the adjacency matrix is computed. To compute also the distance matrix, use the attribute "distance_matrix" with a true value to the new() constructor. attribute_name => attribute_name By default the edge attribute used for distance is "w". You can change that by giving another attribute name with the "attribute_name" attribute to new() constructor. Using this attribute also implicitly causes the distance matrix to be computed. Object Methods is_adjacent($u, $v) Return true if the vertex $v is adjacent to vertex $u, or false if not. distance($u, $v) Return the distance between the vertices $u and $v, or "undef" if the vertices are not adjacent. adjacency_matrix Return the adjacency matrix itself (a list of bitvector scalars). vertices Return the list of vertices (useful for indexing the adjacency matrix). ALGORITHM
The algorithm used to create the matrix is two nested loops, which is O(V**2) in time, and the returned matrices are O(V**2) in space. SEE ALSO
Graph::TransitiveClosure, Graph::BitMatrix AUTHOR AND COPYRIGHT
Jarkko Hietaniemi jhi@iki.fi LICENSE
This module is licensed under the same terms as Perl itself. perl v5.10.0 2005-04-16 Graph::AdjacencyMatrix(3pm)
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