joey711/biomformat-oldfork

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biomformat-oldfork's Issues

Use automagic table structure in jsonlite

Current JSON approach is unnecessary with jsonlite, where the table structure will be interpreted automatically, and most-likely in a much more efficient manner than the way it is handled now (always start as list?)

This is the last dangling aspect of a previous issue, which should now be considered closed:

joey711/biomformat0#2

Read numeric class, default to integers, when importing biom/HDF5 file in R

Borrowed migrated from previous post:

joey711/biomformat0#3

Add script to test write_biom output based on python lib

Script would go in inst/scripts and be run as external shell command (e.g. system) from a new unit test, creating an implicit Suggests-type testing dependency on the availability of an up-to-date biom-format python library

joey711/biomformat#4 (comment)

write_biom output appears invalid due to improper types in format metadata

"format", "format_url", "type":, "generated_by", "date", "id"s within rows/columns, "matrix_type", etc are all wrapped in lists ([]), whereas the specification states these should be strings: http://biom-format.org/documentation/format_versions/biom-1.0.html

Files created by the write_biom method cannot be parsed by the official biom-format command-line tools, resulting in the error of TypeError: <filename> does not appear to be a BIOM file!

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> library('biomformat')
> packageVersion('biomformat')
[1] ‘1.2.0’
> biom_file <- system.file("extdata", "rich_sparse_otu_table.biom", package = "biomformat")
> x = read_biom(biom_file)
> outfile = tempfile()
> write_biom(x, outfile)
> system(paste0("cat ", outfile) )
{"id":{},"format":["Biological Observation Matrix 1.0.0-dev"],"format_url":["http://biom-format.org"],"type":["OTU table"],"generated_by":["QIIME revision XYZ"],"date":["2011-12-19T19:00:00"],"rows":[{"id":["GG_OTU_1"],"metadata":{"taxonomy":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia","s__"]}},{"id":["GG_OTU_2"],"metadata":{"taxonomy":["k__Bacteria","p__Cyanobacteria","c__Nostocophycideae","o__Nostocales","f__Nostocaceae","g__Dolichospermum","s__"]}},{"id":["GG_OTU_3"],"metadata":{"taxonomy":["k__Archaea","p__Euryarchaeota","c__Methanomicrobia","o__Methanosarcinales","f__Methanosarcinaceae","g__Methanosarcina","s__"]}},{"id":["GG_OTU_4"],"metadata":{"taxonomy":["k__Bacteria","p__Firmicutes","c__Clostridia","o__Halanaerobiales","f__Halanaerobiaceae","g__Halanaerobium","s__Halanaerobiumsaccharolyticum"]}},{"id":["GG_OTU_5"],"metadata":{"taxonomy":["k__Bacteria","p__Proteobacteria","c__Gammaproteobacteria","o__Enterobacteriales","f__Enterobacteriaceae","g__Escherichia","s__"]}}],"columns":[{"id":["Sample1"],"metadata":{"BarcodeSequence":["CGCTTATCGAGA"],"LinkerPrimerSequence":["CATGCTGCCTCCCGTAGGAGT"],"BODY_SITE":["gut"],"Description":["human gut"]}},{"id":["Sample2"],"metadata":{"BarcodeSequence":["CATACCAGTAGC"],"LinkerPrimerSequence":["CATGCTGCCTCCCGTAGGAGT"],"BODY_SITE":["gut"],"Description":["human gut"]}},{"id":["Sample3"],"metadata":{"BarcodeSequence":["CTCTCTACCTGT"],"LinkerPrimerSequence":["CATGCTGCCTCCCGTAGGAGT"],"BODY_SITE":["gut"],"Description":["human gut"]}},{"id":["Sample4"],"metadata":{"BarcodeSequence":["CTCTCGGCCTGT"],"LinkerPrimerSequence":["CATGCTGCCTCCCGTAGGAGT"],"BODY_SITE":["skin"],"Description":["human skin"]}},{"id":["Sample5"],"metadata":{"BarcodeSequence":["CTCTCTACCAAT"],"LinkerPrimerSequence":["CATGCTGCCTCCCGTAGGAGT"],"BODY_SITE":["skin"],"Description":["human skin"]}},{"id":["Sample6"],"metadata":{"BarcodeSequence":["CTAACTACCAAT"],"LinkerPrimerSequence":["CATGCTGCCTCCCGTAGGAGT"],"BODY_SITE":["skin"],"Description":["human skin"]}}],"matrix_type":["sparse"],"matrix_element_type":["int"],"shape":[5,6],"data":[[0,2,1],[1,0,5],[1,1,1],[1,3,2],[1,4,3],[1,5,1],[2,2,1],[2,3,4],[2,5,2],[3,0,2],[3,1,1],[3,2,1],[3,5,1],[4,1,1],[4,2,1]]}> 

Lose metadata colnames when writing biom object to file

I noticed recently that I lost my metadata column names (both sample_metadata() and observation_metadata() ) after writing a biom object to file and reading it back in with read_biom(). I've tracked it down to the way jsonlite::toJSON() within biomformat::write_biom() writes the json file. The column names are lost while writing. I haven't yet figured out what modifications of arguments in jsonlite::toJSON() need to be made to fix the issue. However, I found that with RJSONIO::toJSON() the issue is resolved.

Here's a demo of the issue in this gist with an example adapted from the write_biom() help docs: https://gist.github.com/altrickter/978e23dd3bded3cabd75286b994a6a0f.