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Binning without mapping #226

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meren opened this Issue Nov 17, 2015 · 2 comments

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meren commented Nov 17, 2015

I.e., ability to bin when you only have a bunch of contigs, and no metagenomic data to map on to them.

Although clearly this is not ideal, this should be possible for benchmarking or other types of experimental purposes.

For instance, if someone wants to download N genomes from the NCBI, chop them up into random short reads, assemble them back, and try to bin them using the anvi'o interactive interface based on TNF alone, they should be able to do it.

@meren meren added this to the v2.0.0 milestone Jun 6, 2016

@meren meren self-assigned this Jun 6, 2016

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meren commented Jun 6, 2016

Because the weather outside was unbearably gorgeous for my mental health, I have been working on this issue during the weekend.

I realized that the most elegant solution that works well with the codebase is to add an option to generate a blank anvi'o profile, that holds no views or data, but serves for any other purpose.

Commits to facilitate this will follow.

meren added a commit that referenced this issue Jun 6, 2016

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meren added a commit that referenced this issue Jun 6, 2016

profiler += the ability to generate blank profiles
related to #226. yet another example to show the extent of flexibility
we have with anvi'o's design. very happy.

meren added a commit that referenced this issue Jun 6, 2016

meren added a commit that referenced this issue Jun 6, 2016

meren added a commit that referenced this issue Jun 6, 2016

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meren commented Jun 6, 2016

This works now. Say you have a CONTIGS.db:

$ anvi-profile -c CONTIGS.db -S BLANK_TEST -o BLANK-TEST --blank-profile
$ anvi-interactive -c CONTIGS.db -p BLANK-TEST/PROFILE.db

And this is what you get:

image

With two clusterings avaialble:

image

A blog post is in order!

@meren meren closed this Jun 6, 2016

meren added a commit that referenced this issue Jun 6, 2016

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