For the record: see https://support.bioconductor.org/p/62283 which includes a reply.
> On 25 Oct 2014, at 21:07, Joseph Nathaniel Paulson <jpaul...@umiacs.umd.edu> > wrote: > > Hello, > > I'm in the process of writing a few wrappers for loading and writing out > files in the biom-format > <http://biom-format.org/documentation/format_versions/biom-2.1.html> that > happens to be in HDF5 format. The rhdf5 package is great, but in > particular, the beginning of every file (as an example: > https://github.com/biocore/biom-format/blob/master/examples/rich_sparse_otu_table_hdf5.biom > ) > has missing information that I can get running the command-line version of > hdf5dump > > Running hdf5dump vs. 1.8.7 I'm able to see *creation-date*, *format-url*, > *format-version*, etc (see below). > > However, running h5read/ls on the same object none of these > categories/groups come up. My goal is to get the format-verson, etc groups > that are not showing up. > > > Thank you, > > Joseph Paulson > > > *Example:* > > *# in R* > > *str(h5read("./rich_sparse_otu_table_hdf5.biom","/"))*List of 2 > $ observation:List of 4 > ..$ group-metadata: NULL > ..$ ids : chr [1:5(1d)] "GG_OTU_1" "GG_OTU_2" "GG_OTU_3" > "GG_OTU_4" ... > ..$ matrix :List of 3 > .. ..$ data : num [1:15(1d)] 1 5 1 2 3 1 1 4 2 2 ... > .. ..$ indices: int [1:15(1d)] 2 0 1 3 4 5 2 3 5 0 ... > .. ..$ indptr : int [1:6(1d)] 0 1 6 9 13 15 > ..$ metadata :List of 1 > .. ..$ taxonomy: chr [1:7, 1:5] "k__Bacteria" "p__Proteobacteria" > "c__Gammaproteobacteria" "o__Enterobacteriales" ... > $ sample :List of 4 > ..$ group-metadata: NULL > ..$ ids : chr [1:6(1d)] "Sample1" "Sample2" "Sample3" "Sample4" > ... > ..$ matrix :List of 3 > .. ..$ data : num [1:15(1d)] 5 2 1 1 1 1 1 1 1 2 ... > .. ..$ indices: int [1:15(1d)] 1 3 1 3 4 0 2 3 4 1 ... > .. ..$ indptr : int [1:7(1d)] 0 2 5 9 11 12 15 > ..$ metadata :List of 4 > .. ..$ BODY_SITE : chr [1:6(1d)] "gut" "gut" "gut" "skin" ... > .. ..$ BarcodeSequence : chr [1:6(1d)] "CGCTTATCGAGA" "CATACCAGTAGC" > "CTCTCTACCTGT" "CTCTCGGCCTGT" ... > .. ..$ Description : chr [1:6(1d)] "human gut" "human gut" "human > gut" "human skin" ... > .. ..$ LinkerPrimerSequence: chr [1:6(1d)] "CATGCTGCCTCCCGTAGGAGT" > "CATGCTGCCTCCCGTAGGAGT" "CATGCTGCCTCCCGTAGGAGT" "CATGCTGCCTCCCGTAGGAGT" ... > >> sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1]* rhdf5_2.10.0 * BiocInstaller_1.16.0 > loaded via a namespace (and not attached): > [1] tools_3.1.0 zlibbioc_1.12.0 > > *# Terminal * > > *./hdf5-1.8.7-mac-intel-x86_64-static/bin/h5dump > ./rich_sparse_otu_table_hdf5.biom *HDF5 "./rich_sparse_otu_table_hdf5.biom" > { > GROUP "/" { > ATTRIBUTE "creation-date" { > DATATYPE H5T_STRING { > STRSIZE H5T_VARIABLE; > STRPAD H5T_STR_NULLTERM; > CSET H5T_CSET_ASCII; > CTYPE H5T_C_S1; > } > DATASPACE SCALAR > DATA { > (0): "2014-07-29T16:16:36.617320" > } > } > ATTRIBUTE "format-url" { > DATATYPE H5T_STRING { > STRSIZE H5T_VARIABLE; > STRPAD H5T_STR_NULLTERM; > CSET H5T_CSET_ASCII; > CTYPE H5T_C_S1; > } > DATASPACE SCALAR > DATA { > (0): "http://biom-format.org" > } > } > ATTRIBUTE "format-version" { > DATATYPE H5T_STD_I64LE > DATASPACE SIMPLE { ( 2 ) / ( 2 ) } > DATA { > (0): 2, 1 > } > } > ATTRIBUTE "generated-by" { > DATATYPE H5T_STRING { > STRSIZE H5T_VARIABLE; > STRPAD H5T_STR_NULLTERM; > CSET H5T_CSET_ASCII; > CTYPE H5T_C_S1; > } > DATASPACE SCALAR > DATA { > (0): "example" > } > } > ATTRIBUTE "id" { > DATATYPE H5T_STRING { > STRSIZE H5T_VARIABLE; > STRPAD H5T_STR_NULLTERM; > CSET H5T_CSET_ASCII; > CTYPE H5T_C_S1; > } > DATASPACE SCALAR > DATA { > (0): "No Table ID" > } > } > ATTRIBUTE "nnz" { > DATATYPE H5T_STD_I64LE > DATASPACE SCALAR > DATA { > (0): 15 > } > } > ATTRIBUTE "shape" { > DATATYPE H5T_STD_I64LE > DATASPACE SIMPLE { ( 2 ) / ( 2 ) } > DATA { > (0): 5, 6 > } > } > ATTRIBUTE "type" { > DATATYPE H5T_STRING { > STRSIZE H5T_VARIABLE; > STRPAD H5T_STR_NULLTERM; > CSET H5T_CSET_ASCII; > CTYPE H5T_C_S1; > } > DATASPACE SCALAR > DATA { > (0): "otu table" > } > } > ..... > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel