Hi monks,

I have a dataset that consists of a bunch of elements (DNA sequences) that are compared in an all-against-all manner. In case it is relevant, the matches are not necessarily symmetric, so just because A matches B does not guarantee that B will match A. The output looks like this, where each line indicates a match between the sequence in column A and the sequence in column B based on my search criteria:

Contig1  Contig2
Contig1  Contig3
Contig2  Contig1
Contig2  Contig3
Contig3  Contig1
Contig3  Contig2
Contig3  Contig4
Contig4  Contig3
Contig4  Contig5
Contig6  Contig7
Contig7  Contig6
Contig8  Contig9
Contig9  Contig10
Contig10 Contig8
Contig10 Contig11
Contig11 Contig10

[download]

I want to divide this list into groups where a group consists of all the elements that are connected by at least one edge (including non-reciprocal edges). So in the example data, I would have three groups:

Group1: Contig1 Contig2 Contig3 Contig4 Contig5
Group2: Contig6 Contig7
Group3: Contig8 Contig9 Contig10 Contig11

[download]

I am at a lost to figure out an efficient way to do this in Perl, and any help would be greatly appreciated.

In reply to Finding all connected nodes in an all-against-all comparison by Anonymous Monk

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