Convert from PSL to MAF

Question

[anovak]

Hello,

I am looking for a tool thgat can convert some PSL alignments to MAF format. Since MAF includes the sequence and PSL does not, I imagine that I would also need to provide some FASTA or 2bit files to make it work.

Does such a tool exist? Or do I need to write my own?

Answer 1

[anovak]

I have written such a tool, which is available here.

It requires a version of BioPython that can write MAF files, like this one, at least until this pull request or something like it is merged.

[FatihSarigol]

Cool! For anyone with an issue with BioPython, here is an alternative from CGAT: https://github.com/CGATOxford/cgat/blob/master/CGAT/scripts/psl2gff.py