Reverse complement of selective sequences in a maf file

Question

[RoryC]

I'm working with a maf file that contains a mix of blocks aligned to a reference sequence on the + strand and blocks aligned to a reference sequence on the - strand. I'd like to use a program which will only work if all reference sequences are on the + strand, and hence I need to produce the reverse complement for all sequences in blocks which are aligned to a - strand reference. Does anyone have any idea of how to do this?

I'm aware of the Galaxy tool "Reverse Complement" but this doesn't seem to be selective, simply giving the reverse complement of everything in the file. One option would be to extract the blocks aligned to a - strand sequence and then use this tool, but if anyone knows of a more efficient way I'd be extremely grateful.

Thanks, Rory

Answer 1

[RoryC]

Hi, I found another program which did exactly what I needed. If anyone else comes across this question with a similar problem then mafTools has a program called mafStrander:

https://github.com/dentearl/mafTools/tree/master/mafStrander