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marbl / harvest

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Generating a whole genome POA #7

Open iqbal-lab opened 9 years ago

iqbal-lab commented 9 years ago

Hi Guys I'd like to be able to take a Harvest core genome MSA + the non-core bits that were cut out, and make a partial order alignment. i.e. I'd like something like

block {a,b,c} block {d,e,f} block {h,i,j} block

where the blocks are the core MSA, and a,b,c are the sequences that the various genomes have connecting the blocks iei I don't care about aligning the connecting sequence joining the bits of core genome.

Is that something Harvest can generate??

cheers

Zam

iqbal-lab commented 9 years ago

Ping!

treangen commented 9 years ago

hi Zam,

Ping!

apologies for the delay!

Is that something Harvest can generate??

This is something that could be generated but is not currently available as Harvest output. I've started looking into modifying the current unaligned output to generate this & should have something available soon.

iqbal-lab commented 9 years ago

Hey Todd - thanks so much for such a positive reply!! :-)

On 4 June 2015 at 11:31, Todd J Treangen notifications@github.com wrote:

hi Zam,

Ping!

apologies for the delay!

Is that something Harvest can generate??

This is something that could be generated but is not currently available as Harvest output. I've started looking into modifying the current unaligned output to generate this & should have something available soon.

— Reply to this email directly or view it on GitHub https://github.com/marbl/harvest/issues/7#issuecomment-108832653.

iqbal-lab commented 9 years ago

Ping again! Perfectly ok to hear that this is not top priority, and not going to happen til October or whatever, but it would be good to get a rough sense of scale if possible (so I can decide whether to wait or find an alternate solution) cheers Zam

treangen commented 9 years ago

hi Zam,

thanks for the ping & my apologies for the delay in getting back.

I hope to have something ready relatively soon (by early September), and an official release including this new feature (among other updates) is tentatively planned for early October. Will keep you posted.

best,

Todd

iqbal-lab commented 9 years ago

Ping!

thorellk commented 9 years ago

I'm also very interested in this, good to hear that it is already being attended to :)

treangen commented 9 years ago

thanks for the ping/reminder Zam, still working on finalizing new release with prelim support for this, hope to have something for you soon, stay tuned!

iqbal-lab commented 9 years ago

Thanks Todd!

iqbal-lab commented 8 years ago

Ahem!