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Hello,
We are in the process of implementing changes in some of our applications to support biom 2 and have a few questions about it.
1. Where can I find upgrade instructions?
2. Our code looks as fol…
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Hello,
I have code that was working in biom1 and now have to modify to work in biom2.
It was using BiomTable.iterObservations as follows but now in biom2 iterObservations is not working.
What i…
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Hi everyone,
(Apologies if these are already known/in-progress issues or better posted on the user forum - thought they might be useful here)
## Installation Steps
I have been working on setting up …
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Just got this using ``predict_metagenomes.py -i foo -o bar -a NSTI --with_confidence'
``` bash
14:35:21 (mcdonadt@compy):Rosenbaum$ cat /home/mcdonadt/rosen_QQO.e497130
Traceback (most recent call la…
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In the Help documentation on the web site, there is some redundant wording
"If you want to visualize biological data currently formatted as a tab-delimited text file (e.g. the style of OTU tables pro…
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Hello,
I am encountering a problem in the biom2 environment.
Traceback (most recent call last):
File "./scripts/scriptConvertBetweenBIOMAndPCL.py", line 55, in
abndTable.funcWriteToFile(args.…
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12s to parse a 240MB file. Takes ~153ms to read it without parsing. (note, this is of course taking advantage of OS buffers but that is true for parsing and flat read). Profile snapshot below
``` pyt…
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Although in preliminary stage and no official release, `KbaseKit` will provide a way to import data directly from MG-RAST in R.
MG-RAST:
http://metagenomics.anl.gov/
The development repository is o…
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As a possible extension/addition to the current BIOM format, it would be nice to have some way to store relationship data for observations in a table.
For example, a phylogenetic tree showing evoluti…
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If you run:
`biom convert -i test.txt -o new_otu_table.biom --to-hdf5 --table-type="OTU table"`
you will get:
```
File "biom-format/biom/table.py", line 3290, in vlen_list_of_str_formatter
dat…