provide taxonomy operations that work on semicolon-separated lineages #2185
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(this came up during the discussion of |
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Implemented in #2333 - so, for example, the new summarize command would print out: and works as well. |
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Nov 14, 2022
This PR adds a `tax summarize` command per #2212. It also: * tackles native loading of with-lineages files produced by `tax annotate` as taxonomy spreadsheets (#2185) * improves error reporting output for wonky unicode formatted tax CSV files for #2326 Tackles #2212 Tackles #2185 Tackles parts of #2326 ## TODO - [x] tests! - [x] docs! - [x] check desired output format against christy e-mail - [x] provide "linting" style output? - punted to #2361 - [x] maybe we want to use this command, or a separate command, to compare b/t a set of signatures (or a manifest...) and a set of taxonomies? e.g. `tax crosscheck --db db --taxonomy <taxonomy>` that will tell us which identifiers don't have taxonomy, and which taxonomy entries don't have sketches? - punted to #2361 ## Example output Running on a traditional taxonomy file: ``` % sourmash tax summarize gtdb-rs202.taxonomy.v2.db == This is sourmash version 4.5.0. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == loading taxonomies... ...loaded 258406 entries. num idents: 258406 rank superkingdom: 2 distinct identifiers rank phylum: 169 distinct identifiers rank class: 419 distinct identifiers rank order: 1312 distinct identifiers rank family: 3264 distinct identifiers rank genus: 12888 distinct identifiers rank species: 47894 distinct identifiers ``` On a gather-with-lineages file: ``` % sourmash tax summarize SRR606249-k31.x.gtdb.gather.with-lineages.csv == This is sourmash version 4.5.0. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == loading taxonomies... ...loaded 84 entries. num idents: 84 rank superkingdom: 2 distinct identifiers rank phylum: 25 distinct identifiers rank class: 32 distinct identifiers rank order: 42 distinct identifiers rank family: 52 distinct identifiers rank genus: 60 distinct identifiers rank species: 84 distinct identifiers ``` On the bad CSV file from #2326 - ``` % sourmash tax summarize /Users/t/Downloads/cheesegenomes.lineages.csv == This is sourmash version 4.5.0. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == loading taxonomies... ERROR while loading taxonomies! cannot read taxonomy assignments from '/Users/t/Downloads/cheesegenomes.lineages.csv': No taxonomic identifiers found; headers are '\ufeffident','taxid','superkingdom','phylum','class','order','family','genus','species','strain' ``` ## CSV output of per-rank information With CSV output, ``` % sourmash tax summarize gtdb-rs207.taxonomy.sqldb -o aaa.csv == This is sourmash version 4.5.0. == == Please cite Brown and Irber (2016), doi:10.21105/joss.00027. == loading taxonomies... ...loaded 317542 entries. num idents: 317542 rank superkingdom: 2 distinct identifiers rank phylum: 189 distinct identifiers rank class: 481 distinct identifiers rank order: 1593 distinct identifiers rank family: 4107 distinct identifiers rank genus: 16686 distinct identifiers rank species: 65703 distinct identifiers now calculating detailed lineage counts... ...done! saved 88761 lineage counts to 'aaa.csv' ``` and `aaa.csv` looks like: | | rank | count | lineage | |---:|:-------------|--------:|:--------------------------------------------------------------------------------------------------------------| | 0 | superkingdom | 311480 | d__Bacteria | | 1 | phylum | 141114 | d__Bacteria;p__Proteobacteria | | 2 | class | 121804 | d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria | | 3 | order | 74108 | d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales | | 4 | family | 63971 | d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae | | 5 | phylum | 61795 | d__Bacteria;p__Firmicutes | | 6 | class | 61794 | d__Bacteria;p__Firmicutes;c__Bacilli | | 7 | order | 32177 | d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales | | 8 | phylum | 28532 | d__Bacteria;p__Actinobacteriota | | 9 | genus | 27205 | d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Escherichia |
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semicolon-separated lineages and gather |
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when we use
sourmash tax annotateon gather results, we produce a column with semicolon-separated lineages in it. we don't have many (any?) sourmash subcommands that natively ingest that format, although we do have some parsing code here #2041 for metacoder.might be nice to think about tooling that easily interconverts between semicolon separated lineages and comma separated lineages, or something.
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