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andrewrech · Jul 6, 2022 · 42eb1ea · 42eb1ea
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: antigen.garnish
 Title: Tumor neoantigen prediction
-Version: 2.3.0
+Version: 2.3.1
 Authors@R:
     c(person(given = c("Lee", "P."),
              family = "Richman",

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# antigen.garnish 2.3.1
+
+Bugfix:
+
+- errors parsing rare MHCII alleles for netMHC tools
+
 # antigen.garnish 2.3.0
 
 Bugfix:

diff --git a/README.md b/README.md
@@ -26,9 +26,9 @@ Two methods exist to run `antigen.garnish`:
 ### Docker
 
 ```sh
-docker pull andrewrech/antigen.garnish:2.3.0
+docker pull andrewrech/antigen.garnish:2.3.1
 
-cID=$(docker run -it -d andrewrech/antigen.garnish:2.3.0 /bin/bash)
+cID=$(docker run -it -d andrewrech/antigen.garnish:2.3.1 /bin/bash)
 ```
 
 [Download](https://services.healthtech.dtu.dk/software.php) netMHC binaries (academic license): NetMHC 4.0, NetMHCpan 4.1b, NetMHCII 2.3, NetMHCIIpan 4.0.

diff --git a/antigen.garnish.pdf b/antigen.garnish.pdf
diff --git a/inst/extdata/src/antigen.garnish.flowchart.R b/inst/extdata/src/antigen.garnish.flowchart.R
diff --git a/inst/extdata/src/antigen.garnish_transcript_db.R b/inst/extdata/src/antigen.garnish_transcript_db.R
@@ -114,7 +114,7 @@ make_refseq_db <- function(txt) {
   1:length(l) %>% lapply(function(i) {
     print(i)
     ids <- l[[i]] %>% paste(collapse = ",")
-    glue::glue("http 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id={ids}&retmode=xml' > rs{i}.xml") %>% system()
+    paste0("http 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=", ids, "&retmode=xml' > rs", i, ".xml") %>% system()
   })
 
   # extract RefSeq IDm cDNA,  and peptide sequence from .xml
@@ -140,7 +140,7 @@ make_refseq_db <- function(txt) {
 
           sub <- x %>%
             # move to sequence record ancestor corresponding to transcript ID
-            xml2::xml_find_all(glue::glue("//GBSeq_accession-version[text()='{id}']/ancestor::GBSeq"))
+            xml2::xml_find_all(paste0("//GBSeq_accession-version[text()='", id, "']/ancestor::GBSeq"))
 
           peptide <- sub %>%
             # find translation entry