How to use MCScanX's result in jcvi?

[phil622]

First,thanks for this wonderful tool This is my question: I transform the .collinearity file from MCScanX to .anchor file use this command:

python -m jcvi.compara.synteny fromaligns mc.collinearity

But the .anchor file only get 2 column and not produce the score column, so i get this error in next step：

not enough values to unpack (expected 3, got 2)

How can i get the right .anchor file from .colinearity file ?

[annerilotter]

I have the same issue. Have you found a solution yet?

[somnya]

Hello,

I did this and it worked: tail -n+12 file.collinearity | sed -E 's/##.+\s(\w+)&(\w+)\s.+/#\1vs#\2/g' | sed -E 's/.+(\w+)\s(\w+)\t(.+)/\1\t\2\t0/g' > blocks.anchor Still, I cannot realize how to get a bed file of syntenic blocks. I'd appreciate it if anyone could help.

Note: I replaced each e value to 0 since MCScan provides a scientific notation not supported by JCVI. Also, please edit the command using your chr prefixes

Tell me if it worked for you.