Update tests and fetch_uniprot

jpquast · Oct 25, 2024 · abf7be4 · abf7be4
1 parent 17a2ed6
commit abf7be4
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Showing 6 changed files with 12 additions and 8 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -4,7 +4,8 @@
 
 * `assign_peptide_type` now takes the `start` argument, containing the start position of a peptide. If a protein does not have any peptide starting at position `1` and there is a peptide starting at position `2`, this peptide will be considered "tryptic" at the N-terminus. This is because the initial Methionine is likely missing due to processing for every copy of the protein and therefore position `2` is the true N-terminus.
 * `extract_metal_binders()` now uses keywords from UniProt as well. In addition, only "enables" GO terms are considered now.
-* 
+* `fetch_uniprot()` received another default column "keyword".
+
 # protti 0.9.1
 
 ## Bug fixes

diff --git a/R/barcode_plot.R b/R/barcode_plot.R
@@ -120,7 +120,7 @@ barcode_plot <- function(data,
         xmin = ({{ start_position }} - 1) / {{ protein_length }} * 100,
         fill = {{ colouring }}
       ),
-      size = 0.7
+      linewidth = 0.7
     ) +
     {
       if (is.numeric(dplyr::pull(data, {{ colouring }}))) {

diff --git a/R/fetch_uniprot.R b/R/fetch_uniprot.R
@@ -53,7 +53,8 @@ fetch_uniprot <-
              "ft_binding",
              "cc_cofactor",
              "cc_catalytic_activity",
-             "xref_pdb"
+             "xref_pdb",
+             "keyword"
            ),
            batchsize = 200,
            max_tries = 10,

diff --git a/man/extract_metal_binders.Rd b/man/extract_metal_binders.Rd
diff --git a/man/fetch_uniprot.Rd b/man/fetch_uniprot.Rd
diff --git a/tests/testthat/test-fetch_extract_and_enrichment_functions.R b/tests/testthat/test-fetch_extract_and_enrichment_functions.R
@@ -7,7 +7,7 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
     expect_warning(uniprot <- fetch_uniprot(unis))
     expect_is(uniprot, "data.frame")
     expect_equal(nrow(uniprot), 9)
-    expect_equal(ncol(uniprot), 17)
+    expect_equal(ncol(uniprot), 18)
   })
 
   proteome <- fetch_uniprot_proteome(organism_id = "83333", columns = c("accession", "go_f", "xref_string"))
@@ -481,7 +481,8 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
       columns = c(
         "ft_binding",
         "cc_cofactor",
-        "cc_catalytic_activity"
+        "cc_catalytic_activity",
+        "keyword"
       )
     )
 
@@ -495,7 +496,7 @@ if (Sys.getenv("TEST_PROTTI") == "true") {
     )
 
     expect_is(metal_info, "data.frame")
-    expect_equal(ncol(metal_info), 20)
+    expect_equal(ncol(metal_info), 21)
     expect_equal(nrow(metal_info), 35)
   })