How to know which reactions have been added for gap-filling?

cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction

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How to know which reactions have been added for gap-filling? #124

Closed PolTorrentTornos closed 3 years ago

PolTorrentTornos commented 3 years ago

Hi All, I didn't get GAP_FILL tags when I didn't specify any medium (-g M9,LB...), only when I did specify them. I'm assuming that even if I don't specify any growth medium CarveMe does gap-filling. How can I then know which reaction have been added as for gap-filling?

Best, Pol.

P.S: I also added this comment in a closed issue with a similar topic

filrot commented 3 years ago

The gap filled reactions are not associated with any genes, so I think you could filter them out using that as a criterion. Example with cobrapy: [r for r in model.reactions if (not len(r.genes) and not r in model.boundary)] to find non-boundary reactions without genes.