Merge pull request #7 from brendanf/amplicon_extract

Amplicon extract

.github/workflows/check-bioc.yml

@@ -54,7 +54,6 @@ jobs:
         config:
           - { os: ubuntu-latest, r: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:RELEASE_3_18", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
           - { os: macOS-latest, r: '4.3', bioc: '3.18'}
-          - { os: windows-latest, r: '4.3', bioc: '3.18'}
           ## Check https://github.com/r-lib/actions/tree/master/examples
           ## for examples using the http-user-agent
     env:
@@ -143,6 +142,10 @@ jobs:
           ## Required for tcltk
           brew install xquartz --cask
 
+          ## install infernal
+          brew tap brewsci/bio
+          brew install infernal
+
       - name: Install Windows system dependencies
         if: runner.os == 'Windows'
         run: |
@@ -174,14 +177,19 @@ jobs:
           install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
 
           ## Pass #1 at installing dependencies
+          ## This pass uses AnVIL-powered fast binaries
+          ## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
+          ## The speed gains only apply to the docker builds.
           message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
-          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
+          remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
         continue-on-error: true
         shell: Rscript {0}
 
       - name: Install dependencies pass 2
         run: |
           ## Pass #2 at installing dependencies
+          ## This pass does not use AnVIL and will thus update any packages
+          ## that have seen been updated in Bioconductor
           message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
           remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
         shell: Rscript {0}
@@ -260,7 +268,7 @@ jobs:
         run: R CMD INSTALL .
 
       - name: Build pkgdown site
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
         ## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
@@ -269,12 +277,12 @@ jobs:
         ## makes the git history recognizable by pkgdown.
 
       - name: Install deploy dependencies
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/{{pkgdown_covr_branch}}' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         run: |
           apt-get update && apt-get -y install rsync
 
       - name: Deploy pkgdown site to GitHub pages 🚀
-        if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
+        if: github.ref == 'refs/heads/{{pkgdown_covr_branch}}' && env.run_pkgdown == 'true' && runner.os == 'Linux'
         uses: JamesIves/github-pages-deploy-action@releases/v4
         with:
           clean: false

DESCRIPTION

@@ -19,26 +19,24 @@ Imports:
     ShortRead,
     dplyr,
     futile.logger,
-    inferrnal (>= 0.99.7),
+    inferrnal (>= 0.99.8),
     IRanges,
     methods,
     purrr,
-    readr,
     rlang,
     stats,
     stringr,
     stringi,
     tibble,
     tidyr,
-    tidyselect,
-    utils
+    tidyselect
 Suggests:
     rITSx (>= 0.0.5),
     knitr,
     rmarkdown,
     covr,
     testthat (>= 2.1.0)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 biocViews:
     SequenceMatching,
     ThirdPartyClient,
@@ -55,3 +53,4 @@ Remotes:
     brendanf/rITSx
 Depends: 
     R (>= 4.1)
+Roxygen: list(markdown = TRUE)

NAMESPACE

@@ -1,5 +1,19 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(extract_LSU,MultipleAlignment)
+S3method(extract_LSU,character)
+S3method(extract_rf_region,XString)
+S3method(extract_rf_region,character)
+S3method(map_position,MultipleAlignment)
+S3method(map_position,character)
+S3method(protect_names,ShortRead)
+S3method(protect_names,character)
+S3method(protect_names,default)
+S3method(repair_unmatched_secondary_structure,BString)
+S3method(repair_unmatched_secondary_structure,character)
+export(find_amplicon)
+export(find_primer)
+export(gap_fill)
 export(lsux)
 export(merge_5_8S)
 export(repair_unmatched_secondary_structure)

NEWS.md

@@ -1,6 +1,12 @@
 # Development version
 
 * Added tests for most functionality.
+* Reimplemented `truncate_alignment()` using `narrow()` method for Stockholm
+  alignments from `inferrnal` 0.99.8.  It now handles interleaved Stockholm
+  files.
+* Added `find_amplicon()` to locate and mark or extract the region defined by a
+  primer pair. Also exported are helper functions `find_primer()` and
+  `gap_fill()`.
 
 # LSUx 0.99.6