update read.genalex and add tests to fix #128

grunwaldlab · Apr 2, 2017 · ca321db · ca321db
1 parent 7fc9094
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diff --git a/NEWS b/NEWS
@@ -43,6 +43,8 @@ BUG FIX
   (see https://github.com/grunwaldlab/poppr/issues/122).
 * Haplodiploids imported in genalex files will be properly treated 
   (see https://github.com/grunwaldlab/poppr/issues/124).
+* `read.genalex()` will now implicitly check for the correct number of 
+  individuals in the data (see https://github.com/grunwaldlab/poppr/issues/128).
 
 MISC
 ----

diff --git a/R/file_handling.r b/R/file_handling.r
@@ -267,6 +267,16 @@ read.genalex <- function(genalex, ploidy = 2, geo = FALSE, region = FALSE,
     warning(msg, immediate. = TRUE)
   }
   gena      <- gena[data_rows, data_cols]
+  if (nrow(gena) != ninds) {
+    theData <- if (inherits(genalex, "character")) genalex else deparse(substitute(genalex))
+    msg <- paste0("\n The number of rows in your data do not match the number ",
+                 "of individuals specified.",
+                 "\n\t", ninds,      " individuals specified",
+                 "\n\t", nrow(gena), " rows in data",
+                 "\n Please inspect ", theData, " to ensure it's a properly ",
+                 "formatted GenAlEx file.\n")
+    stop(msg)
+  }
   #----------------------------------------------------------------------------#
   # Checking for extra information such as Regions or XY coordinates
   #----------------------------------------------------------------------------#

diff --git a/tests/testthat/test-import.R b/tests/testthat/test-import.R
@@ -62,6 +62,15 @@ A009	7_09_BB	224	97	159	160	133	156	126	119	147	227	261	134
 A006	7_09_BB	224	97	159	160	133	156	126	119	147	235	261	134
 A013	7_09_BB	224	97	163	160	133	156	126	119	147	235	257	134"
 
+bad_genalex <- "1	6	1	6
+Ind	Pop	CHMFc4	
+A004	7_09_BB	224	 
+A002	7_09_BB	224	 
+A011	7_09_BB	224	 
+A009	7_09_BB	224	 
+A006	7_09_BB	224	 
+A013	7_09_BB	224	 "
+
 test_that("basic text connections work", {
 	gen <- read.genalex(textConnection(y), sep = "\t")
 	expect_equivalent(tab(gen), tab(monpop[1:6, drop = TRUE]))
@@ -115,6 +124,17 @@ Ind,Pop,RM127, ,RM22, ,RM22, ,RM127,
   expect_warning(read.genalex(textConnection(f)), "col 7: RM22 -> RM22_1")
 })
 
+test_that("improperly-formatted data causes an error", {
+  skip_on_cran()
+  msg <- "^.+?6 individuals.+?5 rows.+?Please inspect "
+  tcmsg  <- paste0(msg, "textConnection\\(bad_genalex\\).+?$")
+  expect_error(read.genalex(textConnection(bad_genalex), sep = "\t"), tcmsg)
+  f <- tempfile()
+  writeLines(bad_genalex, f)
+  fmsg <- paste0(msg, f, ".+?$")
+  expect_error(read.genalex(f, sep = "\t"), fmsg)
+})
+
 context("Data export tests")
 
 test_that("genclone objects can be saved and restored", {