bioconductor / organism.dplyr Goto Github PK

https://github.com/Biocondcutor/AnnotationFilters

There are filter concepts in S4Vectors, ensembldb, and now here. Shouldn't we have just one? One thing that drove us to implement our own filters rather than re-using ensembldb was the ability to easily generate them programmatically, whereas these are all 'hand-crafted' in EnsemblDb.

Organism.dplyr simplifies the bimap and table structure of org and TxDb packages to a small number of tables, but what are the optimal arrangement and membership of tables? Already Organism.dplyr is much more user-friendly than the org / TxDb / Homo.sapiens packages, so is valuable for that reason alone. Note that the genes(), transcripts(), exons(), and cds() verbs are already contracted to return a GRanges; we have genes_tbl() etc returning tibbles.

Could you please add Atlantic salmon as an annotation file under organism in biocondutor?
https://bioconductor.org/packages/release/BiocViews.html#___Organism
Many thanks in advance

Hi Organism.dplyr maintainer,

According to the Multiple platform build/check report for BioC 3.18,
the Organism.dplyr package has the following problem(s):

o ERROR for 'R CMD build' on nebbiolo2. See the details here:
https://master.bioconductor.org/checkResults/3.18/bioc-LATEST/Organism.dplyr/nebbiolo2-buildsrc.html

Please take the time to address this by committing and pushing
changes to your package at git.bioconductor.org

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e.g., entrez_omim_pm vs ensembl_pm

From the current vignette:

Running src_organism() without a given path will save the sqlite file to a tempdir():

...

It might be more convenient if the default behavior was to write the sqlite into a folder
like the one used for AnnotationHub, with src_organism checking for a relevant database
when invoked. It takes a bit of time to build the database, and if I understand the default behavior correctly, it will be lost when the session ends.

E.g., in test-src_organims-class.R, "mouse" test

> names(mcols(exonsBy(src)[[1]]))
Joining, by = c("ensembl", "tx_id")
[1] "tx_id"     "exon_id"   "exon_name" "exon_rank"
> names(mcols(exonsBy(txdb)[[1]]))
[1] "exon_id"   "exon_name" "exon_rank"

I created two sqlite data bases for testing, and somehow missed example.sqlite! I'll fix this, probably removing example.sqlite and updating vignette / documentation

Hello every time I run:

src<- src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene")

I get the error:

Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name?

Not sure how to resolve this.

> sessionInfo()
R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.6 LTS

Matrix products: default
BLAS/LAPACK: FlexiBLAS OPENBLAS; LAPACK version 3.10.1

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: America/Los_Angeles
tzcode source: system (glibc)

attached base packages:
[1] tools stats4 stats graphics grDevices utils datasets methods base

other attached packages:
[1] tinytex_0.45 viridis_0.6.5 viridisLite_0.4.2
[4] rtracklayer_1.60.0 tidylog_1.0.2 data.table_1.15.4
[7] janitor_2.2.0 stringr_1.5.0 stringi_1.7.12
[10] forcats_1.0.0 readODS_2.2.0 patchwork_1.2.0
[13] ggrepel_0.9.3 ggplot2_3.5.0 RColorBrewer_1.1-3
[16] karyoploteR_1.26.0 regioneR_1.32.0 DOSE_3.26.1
[19] TxDb.Hsapiens.UCSC.hg38.knownGene_3.17.0 GenomicFeatures_1.52.1 GenomicRanges_1.52.0
[22] GenomeInfoDb_1.36.1 AnnotationDbi_1.62.2 IRanges_2.34.1
[25] S4Vectors_0.38.1 Biobase_2.60.0 BiocGenerics_0.46.0
[28] Organism.dplyr_1.28.0 AnnotationFilter_1.24.0 dplyr_1.1.4
[31] biomaRt_2.56.1 BiocManager_1.30.22

loaded via a namespace (and not attached):
[1] rstudioapi_0.14 magrittr_2.0.3 rmarkdown_2.22 BiocIO_1.10.0
[5] zlibbioc_1.46.0 vctrs_0.6.5 memoise_2.0.1 Rsamtools_2.16.0
[9] RCurl_1.98-1.12 base64enc_0.1-3 htmltools_0.5.5 S4Arrays_1.0.4
[13] progress_1.2.3 curl_5.2.1 Formula_1.2-5 htmlwidgets_1.6.2
[17] plyr_1.8.9 lubridate_1.9.3 cachem_1.0.8 GenomicAlignments_1.36.0
[21] lifecycle_1.0.3 pkgconfig_2.0.3 Matrix_1.6-5 R6_2.5.1
[25] fastmap_1.1.1 snakecase_0.11.1 GenomeInfoDbData_1.2.10 MatrixGenerics_1.12.2
[29] digest_0.6.31 colorspace_2.1-0 pkgload_1.3.2 bezier_1.1.2
[33] Hmisc_5.1-0 RSQLite_2.3.1 org.Hs.eg.db_3.17.0 filelock_1.0.2
[37] timechange_0.3.0 fansi_1.0.4 httr_1.4.6 compiler_4.3.1
[41] withr_2.5.0 bit64_4.0.5 htmlTable_2.4.1 backports_1.4.1
[45] BiocParallel_1.34.2 DBI_1.2.2 rappdirs_0.3.3 DelayedArray_0.26.6
[49] rjson_0.2.21 HDO.db_0.99.1 foreign_0.8-84 zip_2.3.0
[53] nnet_7.3-19 glue_1.6.2 restfulr_0.0.15 GOSemSim_2.26.0
[57] grid_4.3.1 checkmate_2.3.1 cluster_2.1.4 reshape2_1.4.4
[61] fgsea_1.26.0 generics_0.1.3 gtable_0.3.4 BSgenome_1.68.0
[65] tidyr_1.3.1 ensembldb_2.24.0 hms_1.1.3 xml2_1.3.4
[69] utf8_1.2.3 XVector_0.40.0 pillar_1.9.0 splines_4.3.1
[73] BiocFileCache_2.8.0 lattice_0.22-6 bit_4.0.5 biovizBase_1.48.0
[77] tidyselect_1.2.1 GO.db_3.17.0 Biostrings_2.68.1 knitr_1.46
[81] gridExtra_2.3 ProtGenerics_1.32.0 SummarizedExperiment_1.30.2 xfun_0.43
[85] matrixStats_1.3.0 lazyeval_0.2.2 yaml_2.3.7 evaluate_0.21
[89] codetools_0.2-20 tibble_3.2.1 qvalue_2.32.0 cli_3.6.1
[93] rpart_4.1.23 munsell_0.5.1 dichromat_2.0-0.1 Rcpp_1.0.10
[97] dbplyr_2.5.0 png_0.1-8 XML_3.99-0.14 parallel_4.3.1
[101] blob_1.2.4 prettyunits_1.1.1 bitops_1.0-7 VariantAnnotation_1.46.0
[105] scales_1.3.0 openxlsx_4.2.5.2 purrr_1.0.1 crayon_1.5.2
[109] clisymbols_1.2.0 bamsignals_1.32.0 rlang_1.1.1 cowplot_1.1.1
[113] fastmatch_1.1-3 KEGGREST_1.40.0`

The following should work

src = src_organism(dbpath=hg38light())
filter = GRangesFilter(GenomicRanges::GRanges("chr8:18391245-18401218"))
exons(src, filter)

but currently requires

exons(src, list(filter))

There is an error that is occurring in the tests due to new changes to dbplyr. The tests give the following:

         ERROR
        Running the tests in ‘tests/testthat.R’ failed.
        Last 13 lines of output:
          [32] 95456 - 95461 == -5
          [33] 95456 - 95461 == -5
          [34] 95456 - 95461 == -5
          [35] 95456 - 95461 == -5
          [47] 95461 - 95456 ==  5
          ...
   
          ══ testthat results
    ═════════════════════════════════════════════════════════════════════════
          OK: 200 SKIPPED: 0 FAILED: 1
          1. Failure: select (@test-src_organism-select.R#44)
   
          Error: testthat unit tests failed
          In addition: Warning message:
          call dbDisconnect() when finished working with a connection
          Execution halted

it is unpleasant to have to modify select statements when switching to
id_go_all (which has goall, evidenceall, etc.) from id_go (which has go, evidence...)

i'd propose using the same simple field names for both tables