Re: [Samtools-devel] AXT to SAM?

[Dan B. <dan...@gm...>]

Hi Bob,

Yes please do send them along! Anything is better than nothing!

Sorry for missing this reply the first time!


Sincerely,
Dan.

On 8 August 2012 15:29, Bob Harris <rsh...@bx...> wrote:
> Howdy, Dan,
>
> I saw your recent post, below.  You are probably aware that lastz can
> generate SAM directly.  So I am assuming your need to convert AXT is either
> because you have older alignment files in AXT format, or because you have
> some pipeline that post processes last alignments and produces AXT.
>
> I have two python scripts that might be able to do the conversion you want.
> One converts axt to maf, the other converts maf to sam.  If you want these I
> can send them, but with the stipulation that I won't provide any support,
> and I don't provide any guarantees, etc.  Basically these are a couple
> programs I have lying around that I wrote for some specific need years ago.
> I don't know how complete they are, or even if they work well together, and
> I don't have the time to check them (and I don't have any need for these
> myself), though I'd probably be willing to answer a few questions.  I
> suspect they have shortcomings scaling to input files with 100s of millions
> of reads.
>
> That all may sound like it's not worth it, but let me know if you want them.
>
> Bob H
>
>
> You recently posted this to the Samtools-devel mailing list:
>
>> Hello,
>>
>> I need to convert alignments in AXT format from LASTZ [1,2] into SAM. Any
>> tips?
>>
>> [1] http://genome.ucsc.edu/goldenPath/help/axt.html
>> [2]
>> http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html
>
>