Use more extensive scripts [skip ci]

R/answer_bbbq_2.R

@@ -1,5 +1,21 @@
 #' Answer the second BBBQ
 #' @export
 answer_bbbq_2 <- function() {
+  #xml_filename <- system.file("extdata", "short_vs_short.xml", package = "bbbq")
+  xml_filename <- "~/GitHubs/bbbq/scripts_2/short_vs_all.xml"
+  testit::assert(file.exists(xml_filename))
+  x <- xml2::read_xml(xml_filename)
+  x
+  testit::assert(xml2::xml_name(x) == "BlastOutput")
+  xml_iterations <- xml_children(xml_children(x)[9])
+  xml_first_iteration <- xml_children(xml_iterations[1])
 
-}
+  xml_first_hits <- xml_children(xml_first_iteration[5])
+
+  xml_child(xml_children(xml_first_hits), ns = "Hit_def")
+
+  xml2::xml_children(x)
+  xml_children(xml_children(x))
+  xml2::xml_text(x)
+  xml2::xml_find_all(x, ".//baz")
+}

scripts_2/blast_to_xml

@@ -1,3 +1,3 @@
 #!/bin/bash
 
-blastp -query mycobacterium_short.faa -db mycobacterium_short.faa -out short_vs_short.xml -outfmt 5
+blastp -query mycobacterium_short.faa -db mycobacterium_db.faa -out short_vs_all.xml -outfmt 5

scripts_2/blast_to_xml_short

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+blastp -query mycobacterium_short.faa -db mycobacterium_short.faa -out short_vs_short.xml -outfmt 5