Satsuma output format to chain format

Question

[iraun]

Hi there,

I was wondering if there is tool for converting satsuma alignment output format to chain format.

Satsuma output:

• Target sequence name
• First target base
• Last target base
• Query sequence name
• First query base
• Last query base
• Identity orientation

EXAMPLE:

chrX 5947 6164 chrX 9153 chrX 6270 6452 chrX 9472 9360 0.626728 + 9654 0.576923 +

Any help would be appreciated.

Thanks.

[raf.marcondes]

I know this was a long time ago, but anyone got any thoughts? I'm hoping to do the same thing.