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subcommand to generate jplace file from OTU table #215

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@matsen
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matsen commented Jan 28, 2012

QIIME's basic data structure is an OTU table. This data structure holds the results from a collection of samples, in terms of OTU structure with taxonomic information and numbers of reads per OTU.

The best way to get started is probably to go through the QIIME tutorial to step 7. At this point we should have a tree and an OTU table. We would like to turn this into two files. First, a .jplace file with a collection of fake placements, and second, a CSV file mapping read names to specimens. The combination of these two should give an appropriate split placefile. Note what I called a specimen just now is called a "split placefile name" in the pplacer docs and "sample IDs" in the QIIME documentation.

There is something a little funny here, which is that the read names are actually lost in the generation of the OTU table. So we will have to make some up. I suggest <otu number>__<sample ID>.

For each non-empty combination of OTU number and sample ID, a placement should be generated on the pendant edge labeled by the OTU that has zero pendant branch length and zero distal length with the fake "read name" described above. All of these will get put in a .jplace file. Then, the mapping of "read name"s to sample IDs will go in a CSV file.

@metasoarous, could you please go through enough of the tutorial to make a tree and an OTU table using the QIIME virtual box. Then pass these files off to @habnabit and reassign the issue to him.

@metasoarous metasoarous was assigned Jan 28, 2012
@matsen
Owner
matsen commented Jan 28, 2012

I was originally thinking that this would be a script, but I think it should be guppy of_otu_table.

@metasoarous
Collaborator

OTU table output of the QIIME tutorial is located at:

/home/matsengrp/working/csmall/otus.tgz
@habnabit habnabit was assigned Feb 22, 2012
@habnabit habnabit merged commit 6846245 into dev Apr 18, 2012
habnabit added some commits Jul 13, 2012
@habnabit habnabit Adding BIOM support to guppy/rppr.
Anything that reads a placefile is now able to read an OTU table BIOM file with
a tree as if it was a split placefile. Reference packages can also be built by
splitting an OTU table BIOM file into a taxtable and seqinfo file. This allows
taxonomically-annotated analyses to be done on QIIME output.
75c2393
@habnabit habnabit Minor code cleanup. e608cd9
@habnabit habnabit Adding a script for QIIME integration with guppy pca.
QIIME can do 2D and 3D plots of PCoA data, but the output format for guppy pca
is slightly different from what QIIME wants.
b7f4acc
@habnabit habnabit reopened this Jul 13, 2012
@habnabit habnabit added a commit that closed this pull request Aug 22, 2012
@habnabit habnabit Merge branches '215-biom-support', '277-multivariate-hypergeometric-r…
…arefy' and '278-rarefact-split-placefile' into dev

Closes #215; closes #276; closes #277; closes #278.
8bbf93f
@habnabit habnabit closed this in 8bbf93f Aug 22, 2012
@cmccoy cmccoy added a commit that referenced this pull request Feb 28, 2013
@cmccoy cmccoy Fix some bugs in extract_taxonomy_from_biom.py
* Add genus and species to ranks, rank_order
* Name nodes using full lineage in case of name reuse at a rank
* Uncomment a required import

No changelog entry: not yet released. See #215
ffdb278
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