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chrisquince / STRONG

Strain Resolution ON Graphs
MIT License
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Graph simplification removes true paths on single genes #24

Closed chrisquince closed 5 years ago

chrisquince commented 5 years ago

The example data sets I used for testing single gene simplification are all here:

/mnt/gpfs/Hackathon/StrainMetaSim/COG0060

I focussed on the largest component:

component_0.gfa

and tried multiple simplifications. The assignments to known strains are given in the *.ass files.

These can be generated by the Blast.sh and Fasta.sh scripts

snurk commented 5 years ago

Apparently I don't have access to the COG0060 subfolder. @Sebastien-Raguideau can you help?

snurk commented 5 years ago

Ok, it seems like there was a major bug and again to in my own code :( It affected only graphs loaded from GFA (hopefully it is the last bug in my colleague's code there). So, good news is that the "preliminary" simplification step where we are simplifying entire was not affected. Bad news is that cog-level simplification will need rerunning. @chrisquince

snurk commented 5 years ago

I updated the executables in cog_tools2 and tested on the subgraphs that you have been using.