a little quirk (bug?) due to formatting in biom convert

[devonorourke]

Sometimes I have use for .csv formats, others .tsv. Often when I'm working in AMPTK I use .csv formats because I find it easier to filter some things manually.
What I noticed is that if you set the output to .csv format in the amptk filter step, then run amptk taxonomy with that .csv file, you don't generate a .biom file.
It fails, apparently, because the biom convert argument doesn't recognize a comma-separated file! I converted it to a tab-delimited file and it worked just fine.

[devonorourke]

First, please ignore if this was already fixed. I'm using amptk v1.1.4, so not the most up to date...

I wanted to add that in the next step, after the *.biom.tmp file is created and you append the metadata... In my system the default file name it was looking for to find the taxonomy table wasn't right:
The script looked for:

 biom add-metadata -i Mangan.biom.tmp -o Mangan.biom --observation-metadata-fp Mangan.qiime.taxonomy.txt -m mangan.mappingFile.txt --sc-separated taxonomy --output-as-json

But there isn't any Mangan.qiime.taxonomy.txt file. Instead, the default name is Mangan.otu_table.taxonomy.txt. Once I swapped that manually it worked fine.

Cheers!

[nextgenusfs]

Looks like amptk taxonomy is expecting only tab delimited. So I guess I never saw this because I don't ever use csv -- I only added that as a request from Michelle.

[devonorourke]

Michelle is such a trouble maker...
Easy fix anyhow. Thanks.