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HCBravoLab / metagenomeSeq

Statistical analysis for sparse high-throughput sequencing
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load_biom taxonomy strings #10

Closed askerdb closed 10 years ago

askerdb commented 10 years ago

Hi,

There seems to be some problems relating to importing biom files, specifically importing the taxonomy strings correctly. The loaded version is metagenomeSeq_1.7.13, recently installed with install_github().

The load_biom() seem to be making some assumptions about the taxonomy string. We use a wide array of databases because we both have older experiments and non-16S experiments (ITS, LSU, nif etc) so it would be useful if we could either state precisely what the format is or relax it. The otu table i wanted to attach was produced by the greengenes 2010 release. Can i send it to your mail directly?

The load_biom() function assumes the first piece of metadata it sees specifies the length for all

len = length(observation_metadata(obj)[[1]])

Furthermore, for some reason that is not entirely clear to me the call to sapply converts all the strings to numbers

Thanks in advance for help with this, Asker Brejnrod

jnpaulson commented 10 years ago

Certainly, please send it to me directly I and I will write a patch for this.