search

kwongj / roary2fripan

Formats Roary output for viewing in FriPan
GNU General Public License v2.0
10 stars 4 forks source link

Roary add new crap column that needs to be deleted for FriPan #2

Open andersgs opened 7 years ago

andersgs commented 7 years ago

In proteinortho file, Roary now adds a Alg.-Conn. column. It seems to have every gene in the DB. It screws up the pan genome tree, the clustering, and the alignment views.

Deleting that column seems to make things work again.

Anders and Jean.

kwongj commented 7 years ago

Thanks Anders. Do you have an example?

Roary doesn't actually add that Alg.-Conn column - the header is a misnomer.

Fripan takes input in the format of the output from proteinortho, and that Alg.-Conn. column represented "the algebraic connectivity of the respective group to indicate how densely the genes are connected in the orthology graph that was used for clustering". roary2fripan simply reformats the Roary output (gene_presence_absence.csv) to resemble the proteinortho output, so have just used a column that has some value in it.

My tests still seem to be working on the examples I'm using ...

tseemann commented 7 years ago

Are you running roary with -s switch?
"don't split paralogs" This can cause problems, as you get >1 locustag in a cell.

kwongj commented 6 years ago

@andersgs Do you know if this is still an issue? I tried running this recently on a few examples and didn't seem to have any problems.

tseemann commented 6 years ago

Fripan is a total mess right now, sorry. @drpowell