This work tree will attempt to ask some questions about the essentiality of prophage regions in a few bacterial strains of interest to Yoann:
My understanding of Yoann’s goals is not yet complete, I think we will be doing some queries of samples from bioproject PRJNA668602 as well as reinterpreting our previous results of some 5448/M1/NZ131 samples in order to look a little more carefully at the putative prophage regions.
After I grabbed what I think are current assemblies for these genomes, I ran phastaf on them to get the following putative prophage coordinates:
(Note, I need to take a minute and write down the gene IDs therein.)
| Contig | start e | nd OR | Fs |
|---|---|---|---|
| CP000521 | 928530 | 929082 | 1 |
| CP000521 | 1334211 | 1336523 | 3 |
| CP000521 | 1342834 | 1344535 | 3 |
| CP000521 | 1367712 | 1368684 | 2 |
| CP000521 | 1831088 | 1831316 | 1 |
| CP000521 | 2334766 | 2361414 | 27 |
| CP000521 | 2370788 | 2371052 | 1 |
| CP000521 | 2375167 | 2376286 | 1 |
| CP000521 | 2378697 | 2378964 | 1 |
| Contig | start | end | ORFs |
|---|---|---|---|
| CP008776 | 323721 | 324042 | 3 |
| CP008776 | 413106 | 446866 | 36 |
| CP008776 | 450234 | 450704 | 2 |
| CP008776 | 453540 | 453717 | 1 |
| CP008776 | 600591 | 601695 | 1 |
| CP008776 | 659989 | 661129 | 1 |
| CP008776 | 663415 | 691106 | 42 |
| CP008776 | 739785 | 739908 | 1 |
| CP008776 | 817108 | 854441 | 52 |
| CP008776 | 1289907 | 1291212 | 1 |
| CP008776 | 1718455 | 1718650 | 1 |
| Contig | start e | nd OR | Fs |
|---|---|---|---|
| NZ_LS483338 | 318536 | 318857 | 3 |
| NZ_LS483338 | 321542 | 360909 | 58 |
| NZ_LS483338 | 591773 | 592877 | 1 |
| NZ_LS483338 | 697509 | 697632 | 1 |
| NZ_LS483338 | 770603 | 778346 | 11 |
| NZ_LS483338 | 784465 | 789136 | 9 |
| NZ_LS483338 | 792861 | 793047 | 1 |
| NZ_LS483338 | 1202519 | 1203824 | 1 |
| NZ_LS483338 | 1636235 | 1636430 | 1 |
| Contig | start | end | ORFs |
|---|---|---|---|
| CP000829 | 560383 | 561688 | 1 |
| CP000829 | 751629 | 785701 | 39 |
| CP000829 | 1094129 | 1094252 | 1 |
| CP000829 | 1198932 | 1200036 | 1 |
| CP000829 | 1435686 | 1436007 | 3 |
| CP000829 | 1463220 | 1467186 | 7 |
| CP000829 | 1469295 | 1472342 | 2 |
| CP000829 | 1487870 | 1496304 | 20 |
| CP000829 | 1498835 | 1501664 | 5 |
| CP000829 | 1504588 | 1505660 | 3 |
| CP000829 | 1704534 | 1704729 | 1 |
pander::pander(sessionInfo())R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale: LC_CTYPE=en_US.UTF-8, LC_NUMERIC=C, LC_TIME=en_US.UTF-8, LC_COLLATE=en_US.UTF-8, LC_MONETARY=en_US.UTF-8, LC_MESSAGES=en_US.UTF-8, LC_PAPER=en_US.UTF-8, LC_NAME=C, LC_ADDRESS=C, LC_TELEPHONE=C, LC_MEASUREMENT=en_US.UTF-8 and LC_IDENTIFICATION=C
attached base packages: stats4, stats, graphics, grDevices, utils, datasets, methods and base
other attached packages: hpgltools(v.1.0), testthat(v.3.1.8), reticulate(v.1.28), SummarizedExperiment(v.1.28.0), GenomicRanges(v.1.50.2), GenomeInfoDb(v.1.34.9), IRanges(v.2.32.0), S4Vectors(v.0.36.2), MatrixGenerics(v.1.10.0), matrixStats(v.0.63.0), Biobase(v.2.58.0) and BiocGenerics(v.0.44.0)
loaded via a namespace (and not attached): utf8(v.1.2.3), RUnit(v.0.4.32), tidyselect(v.1.2.0), lme4(v.1.1-33), RSQLite(v.2.3.1), AnnotationDbi(v.1.60.2), htmlwidgets(v.1.6.2), grid(v.4.2.0), BiocParallel(v.1.32.6), scatterpie(v.0.1.9), devtools(v.2.4.5), munsell(v.0.5.0), codetools(v.0.2-19), miniUI(v.0.1.1.1), withr(v.2.5.0), colorspace(v.2.1-0), GOSemSim(v.2.24.0), filelock(v.1.0.2), knitr(v.1.42), rstudioapi(v.0.14), DOSE(v.3.24.2), Rdpack(v.2.4), GenomeInfoDbData(v.1.2.9), polyclip(v.1.10-4), farver(v.2.1.1), bit64(v.4.0.5), downloader(v.0.4), rprojroot(v.2.0.3), treeio(v.1.22.0), vctrs(v.0.6.2), generics(v.0.1.3), gson(v.0.1.0), clusterGeneration(v.1.3.7), xfun(v.0.39), BiocFileCache(v.2.6.1), R6(v.2.5.1), doParallel(v.1.0.17), graphlayouts(v.1.0.0), locfit(v.1.5-9.7), gridGraphics(v.0.5-1), bitops(v.1.0-7), cachem(v.1.0.8), fgsea(v.1.24.0), DelayedArray(v.0.24.0), promises(v.1.2.0.1), BiocIO(v.1.8.0), scales(v.1.2.1), ggraph(v.2.1.0), enrichplot(v.1.18.4), gtable(v.0.3.3), sva(v.3.46.0), processx(v.3.8.1), tidygraph(v.1.2.3), rlang(v.1.1.1), genefilter(v.1.80.3), splines(v.4.2.0), rtracklayer(v.1.58.0), lazyeval(v.0.2.2), broom(v.1.0.4), yaml(v.2.3.7), reshape2(v.1.4.4), GenomicFeatures(v.1.50.4), backports(v.1.4.1), httpuv(v.1.6.10), qvalue(v.2.30.0), clusterProfiler(v.4.6.2), tools(v.4.2.0), usethis(v.2.1.6), ggplotify(v.0.1.0), ggplot2(v.3.4.2), ellipsis(v.0.3.2), gplots(v.3.1.3), RColorBrewer(v.1.1-3), jquerylib(v.0.1.4), sessioninfo(v.1.2.2), Rcpp(v.1.0.10), plyr(v.1.8.8), progress(v.1.2.2), zlibbioc(v.1.44.0), purrr(v.1.0.1), RCurl(v.1.98-1.12), ps(v.1.7.5), prettyunits(v.1.1.1), remaCor(v.0.0.11), viridis(v.0.6.3), cowplot(v.1.1.1), urlchecker(v.1.0.1), ggrepel(v.0.9.3), fs(v.1.6.2), variancePartition(v.1.28.9), magrittr(v.2.0.3), data.table(v.1.14.8), mvtnorm(v.1.1-3), pkgload(v.1.3.2), patchwork(v.1.1.2), hms(v.1.1.3), mime(v.0.12), evaluate(v.0.21), xtable(v.1.8-4), HDO.db(v.0.99.1), pbkrtest(v.0.5.2), RhpcBLASctl(v.0.23-42), XML(v.3.99-0.14), gridExtra(v.2.3), compiler(v.4.2.0), biomaRt(v.2.54.1), tibble(v.3.2.1), shadowtext(v.0.1.2), KernSmooth(v.2.23-21), crayon(v.1.5.2), minqa(v.1.2.5), htmltools(v.0.5.5), ggfun(v.0.0.9), mgcv(v.1.8-42), later(v.1.3.1), aplot(v.0.1.10), tidyr(v.1.3.0), DBI(v.1.1.3), tweenr(v.2.0.2), dbplyr(v.2.3.2), MASS(v.7.3-60), rappdirs(v.0.3.3), boot(v.1.3-28.1), Matrix(v.1.5-4), brio(v.1.1.3), cli(v.3.6.1), rbibutils(v.2.2.13), igraph(v.1.4.2), parallel(v.4.2.0), pkgconfig(v.2.0.3), GenomicAlignments(v.1.34.1), plotly(v.4.10.1), xml2(v.1.3.4), foreach(v.1.5.2), ggtree(v.3.6.2), annotate(v.1.76.0), bslib(v.0.4.2), XVector(v.0.38.0), yulab.utils(v.0.0.6), stringr(v.1.5.0), callr(v.3.7.3), digest(v.0.6.31), graph(v.1.76.0), Biostrings(v.2.66.0), rmarkdown(v.2.21), fastmatch(v.1.1-3), tidytree(v.0.4.2), edgeR(v.3.40.2), PROPER(v.1.30.0), GSEABase(v.1.60.0), restfulr(v.0.0.15), curl(v.5.0.0), shiny(v.1.7.4), Rsamtools(v.2.14.0), gtools(v.3.9.4), rjson(v.0.2.21), nloptr(v.2.0.3), lifecycle(v.1.0.3), nlme(v.3.1-162), jsonlite(v.1.8.4), aod(v.1.3.2), desc(v.1.4.2), viridisLite(v.0.4.2), limma(v.3.54.2), fansi(v.1.0.4), pillar(v.1.9.0), lattice(v.0.21-8), KEGGREST(v.1.38.0), fastmap(v.1.1.1), httr(v.1.4.6), pkgbuild(v.1.4.0), survival(v.3.5-5), GO.db(v.3.16.0), glue(v.1.6.2), remotes(v.2.4.2), png(v.0.1-8), iterators(v.1.0.14), pander(v.0.6.5), bit(v.4.0.5), ggforce(v.0.4.1), stringi(v.1.7.12), sass(v.0.4.6), profvis(v.0.3.8), blob(v.1.2.4), caTools(v.1.18.2), memoise(v.2.0.1), dplyr(v.1.1.2) and ape(v.5.7-1)
message("This is hpgltools commit: ", get_git_commit())## If you wish to reproduce this exact build of hpgltools, invoke the following:## > git clone http://github.com/abelew/hpgltools.git## > git reset 3e0de6383ee41f791dac5025f8e6790ddc8072bd## This is hpgltools commit: Mon May 15 12:43:27 2023 -0400: 3e0de6383ee41f791dac5025f8e6790ddc8072bdthis_save <- paste0(gsub(pattern = "\\.Rmd", replace = "", x = rmd_file), "-v", ver, ".rda.xz")
message("Saving to ", this_save)## Saving to index-v20230523.rda.xztmp <- sm(saveme(filename = this_save))