#
# load GOTTCHA assignment
#
dat <- load_edge_assignment(file.path("../test_data/SSputum-dil-DNase-cDNA/gottcha-strDB-b",
"allReads-gottcha-strDB-b.list.txt"), type = 'gottcha')
# columns import test
expect_that( dim(dat)[1], equals(65) )
#rows import test
expect_that( dim(dat)[2], equals(4) )
# col names test
expect_that(colnames(dat), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
# test the specific line of file
# LEVEL TAXA ROLLUP ASSIGNED LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
# species Veillonella parvula 0.0375 10606 12569 396 0 198 1.18508391476523 0.0375168122114549
# [0.0] subset family
species_table <- dplyr::filter( dat, LEVEL == "species")
# [0.1] subset taxa
ent_row <- dplyr::filter( species_table, TAXA == "Haemophilus influenzae")
# [0.2] test
expect_that(ent_row$ABUNDANCE, equals(0.04961472))
#
# test the failure
#
expect_that(load_edge_assignment("../test_data/nonexistentfile.txt", type = 'gottcha'), throws_error())
#
# test an empty file
#
empty_df <- load_edge_assignment("../test_data/an_empty_file.tsv", type = 'gottcha')
expect_that(colnames(empty_df), equals( c("LEVEL", "TAXA", "COUNT", "ABUNDANCE") ) )
expect_that(dim(empty_df)[1], equals(0) )
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