tests/testthat/test-all.R

In berkgurdamar/predatoR: Mutation Impact Prediction Based on Network Properties

library(testthat)
library(predatoR)


# predatoR ----------------------------------------------------------------

testthat::skip_on_os("mac")

info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "XXXXX"),
                               c("2DN2", "B", 6, "GLU", "ALA", "XXXXX")))


test_that("Check final error", {
  expect_error(predatoR(info_df = info_df, gene_name_info = T, network_approach = "all", distance_cutoff = 5))
})


test_that("Check final error", {
  expect_error(predatoR(info_df = info_df, gene_name_info = T, network_approach = "ca", distance_cutoff = 7))
})


info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                               c("2DN2", "B", 6, "GLU", "ALA", "HBB")))


test_that("Check network approach error", {
  expect_error(predatoR(info_df = info_df, gene_name_info = T, network_approach = "null"))
})


test_that("Check exploratory output", {
  expect_true(is.data.frame(predatoR(info_df = info_df, gene_name_info = T, network_approach = "ca", distance_cutoff = 7.2)))
})

info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))
test_that("Check output", {
  expect_true(is.data.frame(predatoR(info_df = info_df, gene_name_info = T, network_approach = "ca", distance_cutoff = 7)))
})


test_that("Check exploratory analysis output", {

  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))
  expect_true(is.data.frame(predatoR(info_df = info_df, gene_name_info = T, n_threads = 2, network_approach = "all", distance_cutoff = 5)))
})

test_that("Check input type", {
  expect_error(predatoR(info_df = as.matrix(info_df), gene_name_info = T),
               "Input should be a data.frame.")
})

test_that("Check input column number", {
  expect_error(predatoR(info_df = info_df, gene_name_info = F),
               "Input data.frame should contain 5 columns; PDB_ID, Chain, Position, Orig_AA and Mut_AA respectively.")
})

test_that("Check input column number", {
  expect_error(predatoR(info_df = info_df[,1:5], gene_name_info = T),
               "Input data.frame should contain 6 columns; PDB_ID, Chain, Position, Orig_AA, Mut_AA and Gene_Name respectively.")
})

test_that("Check output class and thread input", {


  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))

  expect_true(is.data.frame(predatoR(info_df = info_df, gene_name_info = T, n_threads = 2)))
})


test_that("Check false pdb input", {


  info_df <- as.data.frame(rbind(c("2DNNN2", "B", 1, "VAL", "ALA", "HBB")))

  expect_error(predatoR(info_df = info_df, gene_name_info = T, n_threads = 2))
})


test_that("Check no gene name input", {


  info_df <- as.data.frame(rbind(c("2DNNN2", "B", 1, "VAL", "ALA")))

  expect_error(predatoR(info_df = info_df, gene_name_info = F, n_threads = 2))
})


### fix regex
info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "asdad", "ALA", "HBB"),
                               c("2DN2", "B", 6, "GLU", "ALA", "HBB")))

test_that("Check input amino acid names", {
  expect_error(predatoR(info_df = info_df, gene_name_info = T))
})

##

info_df <- as.data.frame(rbind(c("2DN2", "B", 10000, "VAL", "ALA", "HBB"),
                               c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))

test_that("Check if residue included", {

  # expect_message(predatoR(info_df = info_df, gene_name_info = T, n_threads = 1),
  #                "Residue [1-9]\\d* is not included in the PDB structure, it will be removed from the query")
  expect_message(predatoR(info_df = info_df, gene_name_info = T, n_threads = 1))
})


info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "GLU", "ALA", "HBB"),
                               c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))

test_that("Check if residue-amino acid matching", {

  expect_message(predatoR(info_df = info_df, gene_name_info = T, n_threads = 1))
})


info_df <- as.data.frame(rbind(c("2DN2", "B", 5, "VAL", "ALA", "HBB")))


test_that("Check input amino acid names", {

  expect_error(predatoR(info_df = info_df, gene_name_info = T, n_threads = 1))
})



test_that("Check multiple amino acid for one residue message", {


  info_df <- as.data.frame(rbind(c("2DN2_N", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DN2_N", "B", 6, "GLU", "ALA", "HBB"),
                                 c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))
  PDB_ID <- "2DN2"
  tmp_dir <- tempdir()
  tmp_path <- file.path(tmp_dir, paste0(PDB_ID, ".pdb"))
  download.file(bio3d::get.pdb(PDB_ID, URL=TRUE), tmp_path)
  download.file(bio3d::get.pdb("1Z2M", URL=TRUE), file.path(tmp_dir, paste0("1Z2M", ".pdb")))
  pdb_file <- bio3d::read.pdb(tmp_path)

  pdb_file$atom$resid[1070] <- "ASP"

  bio3d::write.pdb(pdb_file, file.path(tmp_dir, paste0(PDB_ID, "_N.pdb")))

  expect_message(predatoR(info_df = info_df, gene_name_info = T, PDB_path = tmp_dir, n_threads = 2, distance_cutoff = 5, network_approach = "all"),
                 "There are multiple amino acids for residue [1-9]\\d* in the PDB file, it will be removed from the query")

})


# read_PDB ----------------------------------------------------------------

test_that("Check local PDB read", {
  PDB_ID <- "1Z2M"
  tmp_dir <- tempdir()
  tmp_path <- file.path(tmp_dir, paste0(PDB_ID, ".pdb"))
  download.file(bio3d::get.pdb(PDB_ID, URL=TRUE), tmp_path)

  expect_true(is.data.frame(read_PDB(PDB_ID = PDB_ID, PDB_path = tmp_dir)))

})


test_that("Check wrong PDB name", {
  expect_message(read_PDB("ACCSCS"),
                 "Couldn't download the PDB file [a-zA-Z]+, it will be removed from the query"
  )
})


test_that("Check wrong path", {
  expect_message(read_PDB("2DN2", PDB_path = "path/"),
                 "Couldn't find the PDB file [A-Za-z0-9_-]+ in the given path, it will be removed from the query"
  )
})

test_that("Check output class", {
  expect_true(is.data.frame(read_PDB("2DN2")))
})

test_that("Check network approach error", {
  expect_error(read_PDB("2DN2", network_approach = "null"))
})

test_that("Check ca only pdb read with download", {
  expect_true(is.data.frame(read_PDB("2DN2", network_approach = "ca")))
})

test_that("Check ca only pdb read with pdb read", {
  PDB_ID <- "1Z2M"
  tmp_dir <- tempdir()
  tmp_path <- file.path(tmp_dir, paste0(PDB_ID, ".pdb"))
  download.file(bio3d::get.pdb(PDB_ID, URL=TRUE), tmp_path)
  expect_true(is.data.frame(read_PDB("2DN2", network_approach = "ca", PDB_path = tmp_dir)))
})

# PDB2connections ---------------------------------------------------------

atom_matrix <- read_PDB("2DN2")

info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                               c("2DN2", "B", 6, "GLU", "ALA", "HBB")))


connections_df <- PDB2connections(atom_matrix, info_df, single_run = TRUE, n_threads = 2)

test_that("Check output class an thread input", {

  expect_true(is.list(connections_df))
})


test_that("Check multiple PDB error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DDD", "B", 6, "GLU", "ALA", "HBB")))

  expect_error(PDB2connections(atom_matrix, info_df, single_run = TRUE),
               "filtered_info_df should contain only one PDB entries")
  expect_error(PDB2connections(atom_matrix, info_df, single_run = FALSE),
               "filtered_info_df should contain only one PDB entries")
})




# eigen_centrality_score --------------------------------------------------

test_that("Check output class", {

  expect_true(is.numeric(eigen_centrality_score(connections_df, info_df)))
  expect_message(eigen_centrality_score(connections_df, info_df),
                 "Eigen Centrality Score:		DONE")
})

test_that("Check multiple PDB error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DDD", "B", 6, "GLU", "ALA", "HBB")))

  expect_error(eigen_centrality_score(connections_df, info_df),
               "filtered_info_df should contain only one PDB entries")
})




# shorteset_path_score ----------------------------------------------------

test_that("Check output class", {

  expect_true(is.numeric(shorteset_path_score(connections_df, info_df)))
  expect_message(shorteset_path_score(connections_df, info_df),
                 "Shortest Path Score:		DONE")
})

test_that("Check multiple PDB error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DDD", "B", 6, "GLU", "ALA", "HBB")))

  expect_error(shorteset_path_score(connections_df, info_df),
               "filtered_info_df should contain only one PDB entries")
})


# betweenness_score -------------------------------------------------------

test_that("Check output class", {

  expect_true(is.numeric(betweenness_score(connections_df, info_df)))
  expect_message(betweenness_score(connections_df, info_df),
                 "Betweenness Score:		DONE")
})

test_that("Check multiple PDB error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DDD", "B", 6, "GLU", "ALA", "HBB")))

  expect_error(betweenness_score(connections_df, info_df),
               "filtered_info_df should contain only one PDB entries")
})



# gnomad_scores -----------------------------------------------------------


test_that("Check output class", {

  expect_true(is.data.frame(gnomad_scores(info_df)))
  expect_message(gnomad_scores(info_df),
                 "GNOMAD Scores:			DONE")
})



test_that("Check column number error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA"),
                                 c("2DN2", "B", 6, "GLU", "ALA")))

  expect_error(gnomad_scores(info_df),
               "Input data.frame should contain at least 6 columns; PDB_ID, Chain, Position, Orig_AA, Mut_AA and Gene_Name ... respectively.")
})



test_that("Check wrong gene name message", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "BRCA"),
                                 c("2DN2", "B", 6, "GLU", "ALA", "BRCA")))

  expect_message(gnomad_scores(info_df))

})


test_that("Check multiple gene info", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "AQP1"),
                                 c("2DN2", "B", 6, "GLU", "ALA", "AQP1")))

  expect_true(is.data.frame(gnomad_scores(info_df)))

})


test_that("Check no gene input returning multiple gene", {
  info_df <- as.data.frame(rbind(c("1A01", "A", 1, "VAL", "ALA", ""),
                                 c("1A01", "A", 6, "GLU", "ALA", "")))

  expect_true(is.data.frame(gnomad_scores(info_df)))
})

test_that("Check no gene input", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", ""),
                                 c("2DN2", "B", 6, "GLU", "ALA", "")))

  expect_true(is.data.frame(gnomad_scores(info_df)))
})

test_that("Check wrong pdb input returning no gene", {
  info_df <- as.data.frame(rbind(c("ASDA", "B", 1, "VAL", "ALA", ""),
                                 c("ASDA", "B", 6, "GLU", "ALA", "")))

  expect_true(is.data.frame(gnomad_scores(info_df)))
})


test_that("Check no gene info in gnomad", {
  info_df <- as.data.frame(rbind(c("1ND5", "B", 1, "VAL", "ALA", ""),
                                 c("1ND5", "B", 6, "GLU", "ALA", "")))

  expect_true(is.data.frame(gnomad_scores(info_df)))
})

test_that("Check multiple gene names from PDB no gnomAD scores", {

  info_df <- as.data.frame(rbind(c("1KJ6", "A", 1, "VAL", "ALA", "")))

  expect_message(gnomad_scores(info_df),
                 "GNOMAD Scores:			DONE")
})


# BLOSUM62_score ----------------------------------------------------------

test_that("Check output class", {

  expect_true(is.numeric(BLOSUM62_score(info_df)))
  expect_message(BLOSUM62_score(info_df),
                 "BLOSUM62 Score:			DONE")
})


# KEGG_pathway_number -----------------------------------------------------

test_that("Check output class", {

  expect_true(is.data.frame(KEGG_pathway_number(info_df)))
  expect_message(KEGG_pathway_number(info_df),
                 "KEGG Pathway Number:		DONE")
})



test_that("Check column number error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA"),
                                 c("2DN2", "B", 6, "GLU", "ALA")))

  expect_error(KEGG_pathway_number(info_df),
               "Input data.frame should contain at least 6 columns; PDB_ID, Chain, Position, Orig_AA, Mut_AA and Gene_Name ... respectively.")
})


# genic_intolerance -------------------------------------------------------

test_that("Check output class", {

  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DN2", "B", 6, "GLU", "ALA", "HBB")))

  expect_true(is.data.frame(genic_intolerance(info_df)))
  expect_message(genic_intolerance(info_df),
                 "Genic Intolerance Score:	DONE")
})



test_that("Check input error message", {

  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "BRCA"),
                                 c("2DN2", "B", 6, "GLU", "ALA", "BRCA")))

  expect_message(genic_intolerance(info_df))
})



test_that("Check column number error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA"),
                                 c("2DN2", "B", 6, "GLU", "ALA")))

  expect_error(genic_intolerance(info_df),
               "Input data.frame should contain at least 6 columns; PDB_ID, Chain, Position, Orig_AA, Mut_AA and Gene_Name ... respectively.")
})

# clique_score ------------------------------------------------------------


atom_matrix <- read_PDB("2DN2")

info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                               c("2DN2", "B", 6, "GLU", "ALA", "HBB")))

connections_df <- PDB2connections(atom_matrix, info_df, single_run = TRUE, n_threads = 2)



test_that("Check multiple PDB error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DDD", "B", 6, "GLU", "ALA", "HBB")))

  expect_error(clique_score(connections_df, info_df, single_run = TRUE),
               "filtered_info_df should contain only one PDB entries")
  expect_error(clique_score(connections_df, info_df, single_run = FALSE),
               "filtered_info_df should contain only one PDB entries")
})


test_that("Check output class", {

  expect_true(is.numeric(clique_score(connections_df, info_df, single_run = TRUE, n_threads = 2)))
})




# degree_score ------------------------------------------------------------




test_that("Check multiple PDB error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DDD", "B", 6, "GLU", "ALA", "HBB")))

  expect_error(degree_score(connections_df, info_df),
               "filtered_info_df should contain only one PDB entries")
})


test_that("Check output class", {

  expect_true(is.numeric(degree_score(connections_df, info_df)))
})





# pagerank_score ----------------------------------------------------------


test_that("Check multiple PDB error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA", "HBB"),
                                 c("2DDD", "B", 6, "GLU", "ALA", "HBB")))

  expect_error(pagerank_score(connections_df, info_df),
               "filtered_info_df should contain only one PDB entries")
})


test_that("Check output class", {

  expect_true(is.numeric(pagerank_score(connections_df, info_df)))
})



# impact_prediction -------------------------------------------------------

filtered_info_df <- as.data.frame(rbind(c("4RFZ", "A", 414, "GLY", "ARG", "BTK")))

colnames(filtered_info_df) <- c("PDB_ID", "Chain", "Position", "Orig_AA", "Mut_AA", "Gene_Name")

atom_matrix <- read_PDB("4RFZ")

edge_list <- PDB2connections(atom_matrix, filtered_info_df, n_threads = 2, single_run = T)

filtered_info_df$degree_z_score <- degree_score(edge_list, filtered_info_df)

filtered_info_df$eigen_z_score <- eigen_centrality_score(edge_list, filtered_info_df)

filtered_info_df$shortest_path_z <- shorteset_path_score(edge_list, filtered_info_df)

filtered_info_df$betweenness_scores_z <- betweenness_score(edge_list, filtered_info_df)

filtered_info_df$clique_z_score <- clique_score(edge_list, filtered_info_df, n_threads = 2, single_run = T)

filtered_info_df$pagerank_z_score <- pagerank_score(edge_list, filtered_info_df)

filtered_info_df <- gnomad_scores(filtered_info_df)

filtered_info_df$blosum62_scores <- as.numeric(BLOSUM62_score(filtered_info_df))

filtered_info_df <- KEGG_pathway_number(filtered_info_df)

filtered_info_df <- genic_intolerance(filtered_info_df)

filtered_info_df <- GO_terms(filtered_info_df)

filtered_info_df <- DisGeNET(filtered_info_df)

filtered_info_df <- gene_essentiality(filtered_info_df)

filtered_info_df <- GTEx(filtered_info_df)

filtered_info_df <- amino_acid_features(filtered_info_df)

final_df <- filtered_info_df


test_that("Check output class", {

  expect_true(is.data.frame(impact_prediction(final_df, )))

})


atom_matrix <- read_PDB("4RFZ", network_approach = "ca")

edge_list <- PDB2connections(atom_matrix, filtered_info_df, n_threads = 2, single_run = T)

filtered_info_df$degree_z_score <- degree_score(edge_list, filtered_info_df)

filtered_info_df$eigen_z_score <- eigen_centrality_score(edge_list, filtered_info_df)

filtered_info_df$shortest_path_z <- shorteset_path_score(edge_list, filtered_info_df)

filtered_info_df$betweenness_scores_z <- betweenness_score(edge_list, filtered_info_df)

filtered_info_df$clique_z_score <- clique_score(edge_list, filtered_info_df, n_threads = 2, single_run = T)

filtered_info_df$pagerank_z_score <- pagerank_score(edge_list, filtered_info_df)

test_that("Check ca output class", {

  expect_true(is.data.frame(impact_prediction(final_df, network_approach = "all", distance_cutoff = 5)))

})

test_that("Check prediction error", {

  expect_error(is.data.frame(impact_prediction(final_df, network_approach = "all", distance_cutoff = 8)))

})

test_that("Check network approach error", {

  expect_error(is.data.frame(impact_prediction(final_df, network_approach = "null")))

})

test_that("Check cutoff error", {

  expect_error(is.data.frame(impact_prediction(final_df, network_approach = "all", distance_cutoff = 7)))

})

# filtered_info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))
#
# colnames(filtered_info_df) <- c("PDB_ID", "Chain", "Position", "Orig_AA", "Mut_AA", "Gene_Name")
#
# atom_matrix <- read_PDB("1Z2M")
#
# edge_list <- PDB2connections(atom_matrix, filtered_info_df, n_threads = 2, single_run = T)
#
# filtered_info_df$degree_z_score <- degree_score(edge_list, filtered_info_df)
#
# filtered_info_df$eigen_z_score <- eigen_centrality_score(edge_list, filtered_info_df)
#
# filtered_info_df$shortest_path_z <- shorteset_path_score(edge_list, filtered_info_df)
#
# filtered_info_df$betweenness_scores_z <- betweenness_score(edge_list, filtered_info_df)
#
# filtered_info_df$clique_z_score <- clique_score(edge_list, filtered_info_df, n_threads = 2, single_run = T)
#
# filtered_info_df$pagerank_z_score <- pagerank_score(edge_list, filtered_info_df)
#
# filtered_info_df <- gnomad_scores(filtered_info_df)
#
# filtered_info_df$blosum62_scores <- as.numeric(BLOSUM62_score(filtered_info_df))
#
# filtered_info_df <- KEGG_pathway_number(filtered_info_df)
#
# filtered_info_df <- genic_intolerance(filtered_info_df)
#
# filtered_info_df <- GO_terms(filtered_info_df)
#
# filtered_info_df <- DisGeNET(filtered_info_df)
#
# filtered_info_df <- gene_essentiality(filtered_info_df)
#
# filtered_info_df <- GTEx(filtered_info_df)
#
# filtered_info_df <- amino_acid_features(filtered_info_df)
#
# final_df <- filtered_info_df
#
#
# test_that("Check output class", {
#
#   expect_true(is.data.frame(impact_prediction(final_df)))
#
# })


# GO_terms ----------------------------------------------------------------

test_that("Check column number error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA"),
                                 c("2DN2", "B", 6, "GLU", "ALA")))

  expect_error(GO_terms(info_df),
               "Input data.frame should contain at least 6 columns; PDB_ID, Chain, Position, Orig_AA, Mut_AA and Gene_Name ... respectively.")
})



test_that("Check output class", {

  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))

  expect_true(is.data.frame(GO_terms(info_df)))
  expect_message(GO_terms(info_df),
                 "GO Term Number:			DONE")
})

# DisGeNET ----------------------------------------------------------------

test_that("Check column number error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA"),
                                 c("2DN2", "B", 6, "GLU", "ALA")))

  expect_error(DisGeNET(info_df),
               "Input data.frame should contain at least 6 columns; PDB_ID, Chain, Position, Orig_AA, Mut_AA and Gene_Name ... respectively.")
})



test_that("Check output class", {

  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))

  expect_true(is.data.frame(DisGeNET(info_df)))
  expect_message(DisGeNET(info_df),
                 "DisGeNET Disease Number:	DONE")
})

# gene_essentiality -------------------------------------------------------

test_that("Check column number error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA"),
                                 c("2DN2", "B", 6, "GLU", "ALA")))

  expect_error(gene_essentiality(info_df),
               "Input data.frame should contain at least 6 columns; PDB_ID, Chain, Position, Orig_AA, Mut_AA and Gene_Name ... respectively.")
})



test_that("Check output class", {

  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))

  expect_true(is.data.frame(gene_essentiality(info_df)))
  expect_message(gene_essentiality(info_df),
                 "Gene Essentiality Score:	DONE")

  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"AAACA")))
  expect_message(gene_essentiality(info_df),
                 "Gene Essentiality Score:	DONE")
})

# GTEx --------------------------------------------------------------------

test_that("Check column number error", {
  info_df <- as.data.frame(rbind(c("2DN2", "B", 1, "VAL", "ALA"),
                                 c("2DN2", "B", 6, "GLU", "ALA")))

  expect_error(GTEx(info_df),
               "Input data.frame should contain at least 6 columns; PDB_ID, Chain, Position, Orig_AA, Mut_AA and Gene_Name ... respectively.")
})



test_that("Check output class", {

  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))

  expect_true(is.data.frame(GTEx(info_df)))
  expect_message(GTEx(info_df),
                 "GTEx Score:			DONE")

  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"AAACA")))
  expect_message(GTEx(info_df),
                 "GTEx Score:			DONE")
})


# amino_acid_features -----------------------------------------------------

test_that("Check output class", {

  info_df <- as.data.frame(rbind(c("1Z2M"	,"A",	21,	"SER",	"ASN",	"ISG15")))

  expect_true(is.data.frame(amino_acid_features(info_df)))
  expect_message(amino_acid_features(info_df),
                 "Amino Acid Features:		DONE")

})