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Top Forums Shell Programming and Scripting awk? adjacency matrix to adjacency list / correlation matrix to list Post 302560848 by stonemonkey on Saturday 1st of October 2011 07:11:32 PM
Old 10-01-2011
awk? adjacency matrix to adjacency list / correlation matrix to list

Hi everyone
I am very new at awk but think that that might be the best strategy for this. I have a matrix very similar to a correlation matrix and in practical terms I need to convert it into a list containing the values from the matrix (one value per line) with the first field of the line (row annotation) && the header of the field (column annotation) and some spaces etc. preceding it.
In more abstract terms, I wish to convert an adjacency matrix into adjacency list, which includes the edge weights. In excel it works fine with =IF(B2>0;$A2&" (gg) "&B$1&" = "&B2;"") and some grep but the datasets became just to big. P.S 0 values should be omitted.
Input
 AAABAC...ZZ
AA100.500.7
AB010.300
AC00100.1
...00010
ZZ00001

Output
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
... (gg) ... = 1
ZZ (gg) ZZ = 1


Thanks a million for your efforts☺.
 

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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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