kwongj / cfml-maskrc Goto Github PK

Hi

I've used your code to mask recombination regions in MSA, and it works really well (thank you!). However, I am currently working with a gene alignment which is in xmfa format. CFML has given me the coordinates of the recombination regions and I was wondering if there is a way to use your code to mask these regions in the xmfa?

Hi,
Im trying to run cfml-maskrc and draw a svg figure, Im using the option: --svgcolour to show the recombinant regions in Red.
I looked to HEX format to this colour #FF0000.
I tried to run the following command and I always received the message that it`s a not valid argument to this option

cfml-maskrc.py --aln clean.full.aln --out cfml_mskrc_Efaecium.aln --symbol ? --regions recregions_efaecium --svg cfml_Efaecium.svg --svgorder order_cfml.list --svgcolour #FF0000 > Efaecium_local.output

cfml-maskrc.py: error: argument --svgcolour: expected one argument

How I should input this argument?