pafnet

PAF (pairwise alignment format) to network/graph format converter. This tool is designed to project PAF alignments (the implied overlap and containment graph) into a network format that can be processed by tools like grappolo and gephi

usage

For instance, to convert into Pajek NET format:

pafnet -n x.paf >x.net

Or to write an edgelist:

pafnet -e x.paf >x.edges

Or, to apply colors to the nodes based on a specifed group name that the sequences in the PAF file are prefixed with, producing GEXF which can be rendered in gephi:

# cat colors.rgb
group1  255     0       0
group2  255     96      0
group3  255     191     0
group4  223     255     0
group5  128     255     0
group6  32      255     0
group7  0       255     64
group8  0       255     159
group9  0       255     255
group10 0       159     255
group11 0       64      255
group12 32      0       255
group13 128     0       255
group14 223     0       255
group15 255     0       191
group16 255     0       96

making GEXF:

pafnet -c colors.rgb -p . -g aln.paf >graph.gexf

The sequence names should look like group3.XXXXXX for this to work.

building

Build using cargo. This is rust :)