Question: Convert from PSL to MAF
2
gravatar for anovak
6.5 years ago by
anovak70
United States
anovak70 wrote:

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?

conversion maf psl • 2.0k views
ADD COMMENTlink modified 5.9 years ago • written 6.5 years ago by anovak70
2
gravatar for anovak
5.9 years ago by
anovak70
United States
anovak70 wrote:

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.

ADD COMMENTlink written 5.9 years ago by anovak70

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

ADD REPLYlink written 23 months ago by FatihSarigol190
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