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medvedevgroup / SibeliaZ

A fast whole-genome aligner based on de Bruijn graphs
http://medvedevgroup.com/
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Feature request: xmfa format #8

Closed matthieu-haudiquet closed 5 years ago

matthieu-haudiquet commented 5 years ago

Hello,

Great software! A lot of tools (ClonalFrameML for ex.) rely on the xmfa format, if it's not too much work maybe you could add it to the possible outputs ?

Best,

iminkin commented 5 years ago

Hi,

Thanks for your interest! It should not be too hard, I will add something in the nearest release (unless there is a ready-made converter).

iminkin commented 5 years ago

Please check out this python script (requires a recent BioPython installation): https://github.com/medvedevgroup/SibeliaZ/blob/smart_seed/SibeliaZ-LCB/maf_to_xmfa.py

It takes MAF as standard input and outputs XMFA to standard output. I will merge this thread to the master soon.

matthieu-haudiquet commented 5 years ago

Thanks a lot! Will try asap