diff --git a/DESCRIPTION b/DESCRIPTION index cae568a..c261ceb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: pavian Type: Package Title: Visualize and analyze metagenomics classification results -Version: 1.1.0 +Version: 1.2.0 URL: https://github.com/fbreitwieser/pavian BugReports: https://github.com/fbreitwieser/pavian/issues Authors@R: person("Florian P", "Breitwieser", email = "fpbreitwieser@gmail.com", role = c("aut", "cre")) diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..00a4007 --- /dev/null +++ b/NEWS.md @@ -0,0 +1,14 @@ +pavian v1.1.0 (Release date: 2021-04-13) +============== + +Changes: + +* Add support of Kraken2-Uniq reports +* Add unit tests for read_report function + +pavian v1.2.0 (Release date: 2021-04-14) +============== + +Changes: + +* Add support of Metaphlan3 reports diff --git a/R/datainput-read_report.R b/R/datainput-read_report.R index 3fedfa5..98f4708 100644 --- a/R/datainput-read_report.R +++ b/R/datainput-read_report.R @@ -392,6 +392,7 @@ read_report <- function(myfile, has_header=NULL, check_file = FALSE) { if (is.null(has_header)) { has_header <- grepl("^[a-zA-Z#%\"]",first.line) } + is_metaphlan3_fmt <- grepl("^#mpa_v3", first.line) is_metaphlan_fmt <- grepl("Metaphlan2_Analysis$", first.line) is_krakenu_fmt <- grepl("^.?%\treads\ttaxReads\tkmers", first.line) is_kaiju_fmt <- grepl("^ *%\t *reads", first.line) @@ -438,6 +439,20 @@ read_report <- function(myfile, has_header=NULL, check_file = FALSE) { tl_order <- order(report$taxLineage) tl_order <- c(tl_order[length(tl_order)],tl_order[-length(tl_order)]) report <- report[tl_order, c("taxLineage", "taxonReads", "cladeReads")] + } else if (is_metaphlan3_fmt) { + report <- tryCatch({ + ## TODO: Having comment_char here causes a problem w/ Metaphlan report!! + + utils::read.table(myfile,sep="\t",header = F, + quote = "",stringsAsFactors=FALSE, + comment.char = "#", nrows = nrows, + col.names = c("taxLineage", "taxID", "cladeReads", "additional_species"), + check.names=FALSE) + }, error = function(x) NULL, warning = function(x) NULL) + if (is.null(report)) { return(NULL); } + + report$taxID <- sub(".*\\|", "", report$taxID) + } else if (has_header) { report <- tryCatch({ ## TODO: Having comment_char here causes a problem w/ Metaphlan report!! @@ -484,17 +499,22 @@ read_report <- function(myfile, has_header=NULL, check_file = FALSE) { dmessage(paste("Warning: File",myfile,"does not have the required format")) return(NULL) } - if (colnames(report)[2] == "Metaphlan2_Analysis") { + if (is_metaphlan_fmt || is_metaphlan3_fmt) { ## Metaphlan report - colnames(report) <- c("taxLineage", "cladeReads") + colnames(report)[1] <- "taxLineage" + colnames(report)[colnames(report) == "Metaphlan2_Analysis"] <- "cladeReads" report <- report[order(report$taxLineage), ] report$taxLineage <- gsub("_"," ",report$taxLineage) report$taxLineage <- gsub(" ","_",report$taxLineage) report$taxLineage <- paste0("-_root|", report$taxLineage) - - report <- rbind( - data.frame(taxLineage=c("u_unclassified","-_root"),"cladeReads"=c(0,100), stringsAsFactors = F), - report) + root_lines <- data.frame(taxLineage=c("u_unclassified","-_root"),"cladeReads"=c(0,100), stringsAsFactors = F) + + if ("taxID" %in% colnames(report)) { + root_lines <- cbind(root_lines, "taxID" = c(0, 1)) + report <- report[, c("taxLineage", "cladeReads", "taxID")] + } + + report <- rbind(root_lines, report) } if (all(c("name","taxRank") %in% colnames(report)) && !"taxLineage" %in% colnames(report)) { diff --git a/README.md b/README.md index 70ad437..95d3149 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,5 @@ Pavian is a interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as -Kraken, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome. +Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome. For more information look at the publication at https://doi.org/10.1093/bioinformatics/btz715 diff --git a/tests/testthat/read_report/input/metaphlan2-report.txt b/tests/testthat/read_report/input/metaphlan2-report.txt new file mode 100644 index 0000000..71e12f7 --- /dev/null +++ b/tests/testthat/read_report/input/metaphlan2-report.txt @@ -0,0 +1,100 @@ +#SampleID Metaphlan2_Analysis +k__Bacteria 100.0 +k__Bacteria|p__Bacteroidetes 92.24896 +k__Bacteria|p__Firmicutes 4.65876 +k__Bacteria|p__Proteobacteria 2.8865 +k__Bacteria|p__Verrucomicrobia 0.18438 +k__Bacteria|p__Actinobacteria 0.0214 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia 92.24896 +k__Bacteria|p__Firmicutes|c__Clostridia 4.47127 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria 2.84571 +k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae 0.18438 +k__Bacteria|p__Firmicutes|c__Negativicutes 0.12083 +k__Bacteria|p__Firmicutes|c__Bacilli 0.04699 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria 0.04079 +k__Bacteria|p__Actinobacteria|c__Actinobacteria 0.0214 +k__Bacteria|p__Firmicutes|c__Erysipelotrichia 0.01967 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 92.24896 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales 4.47127 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales 2.84571 +k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales 0.18438 +k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales 0.12083 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales 0.04699 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales 0.04079 +k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Coriobacteriales 0.0214 +k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales 0.01967 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae 52.87458 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae 27.64625 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae 11.39634 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae 2.2975 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiales_noname 2.23639 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae 1.66251 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae 0.60463 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae 0.34162 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_noname 0.32378 +k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae 0.18438 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Oscillospiraceae 0.16531 +k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Veillonellaceae 0.12083 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae 0.04699 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae 0.04079 +k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Coriobacteriales|f__Coriobacteriaceae 0.0214 +k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae 0.01967 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae 0.00802 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae 0.00469 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae 0.00433 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides 52.87458 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Parabacteroides 27.33306 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes 11.39634 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiales_noname|g__Burkholderiales_noname 2.23639 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Faecalibacterium 1.54101 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia 1.18685 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Subdoligranulum 0.73178 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella 0.60463 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium 0.34162 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_noname|g__Bacteroidales_noname 0.32378 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Odoribacter 0.31319 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_noname 0.22849 +k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Akkermansia 0.18438 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Oscillospiraceae|g__Oscillibacter 0.16531 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus 0.15628 +k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Veillonellaceae|g__Veillonella 0.07793 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Dorea 0.06518 +k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Streptococcaceae|g__Streptococcus 0.04699 +k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Veillonellaceae|g__Dialister 0.04289 +k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pasteurellales|f__Pasteurellaceae|g__Haemophilus 0.04079 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Blautia 0.02572 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus 0.02471 +k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Coriobacteriales|f__Coriobacteriaceae|g__Slackia 0.0214 +k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Erysipelotrichaceae_noname 0.01193 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella 0.00802 +k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Catenibacterium 0.00774 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Oxalobacteraceae|g__Oxalobacter 0.00469 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridiaceae_noname 0.00433 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_cellulosilyticus 28.19471 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Parabacteroides|s__Parabacteroides_merdae 26.66884 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_ovatus 10.9491 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_caccae 8.77088 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_vulgatus 4.86029 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_shahii 4.6638 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_putredinis 3.42932 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_finegoldii 3.06599 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Burkholderiales_noname|g__Burkholderiales_noname|s__Burkholderiales_bacterium_1_1_47 2.23639 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Faecalibacterium|s__Faecalibacterium_prausnitzii 1.54101 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_intestinalis 1.04235 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Subdoligranulum|s__Subdoligranulum_unclassified 0.73178 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Parabacteroides|s__Parabacteroides_distasonis 0.66423 +k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Parasutterella|s__Parasutterella_excrementihominis 0.60463 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidales_noname|g__Bacteroidales_noname|s__Bacteroidales_bacterium_ph8 0.32378 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Porphyromonadaceae|g__Odoribacter|s__Odoribacter_splanchnicus 0.31319 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Lachnospiraceae_noname|s__Lachnospiraceae_bacterium_3_1_46FAA 0.22065 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_rectale 0.19829 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_sp_AP11 0.18603 +k__Bacteria|p__Verrucomicrobia|c__Verrucomicrobiae|o__Verrucomicrobiales|f__Verrucomicrobiaceae|g__Akkermansia|s__Akkermansia_muciniphila 0.18438 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Oscillospiraceae|g__Oscillibacter|s__Oscillibacter_unclassified 0.16531 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Coprococcus|s__Coprococcus_sp_ART55_1 0.15628 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Lachnospiraceae|g__Roseburia|s__Roseburia_hominis 0.1445 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Bacteroidaceae|g__Bacteroides|s__Bacteroides_fragilis 0.0994 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_ventriosum 0.07343 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Rikenellaceae|g__Alistipes|s__Alistipes_indistinctus 0.05119 +k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Veillonellaceae|g__Dialister|s__Dialister_invisus 0.04289 +k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Veillonellaceae|g__Veillonella|s__Veillonella_unclassified 0.04243 diff --git a/tests/testthat/read_report/input/metaphlan3-report.txt b/tests/testthat/read_report/input/metaphlan3-report.txt new file mode 100644 index 0000000..af4ccb8 --- /dev/null +++ b/tests/testthat/read_report/input/metaphlan3-report.txt @@ -0,0 +1,32 @@ +#mpa_v30_CHOCOPhlAn_201901 +#metaphlan metaphlan.fastq.gz --input_type fastq --bowtie2out metaphlan_bowtie2.bz2 -o metaphlan.out +#SampleID Metaphlan_Analysis +#clade_name NCBI_tax_id relative_abundance additional_species +k__Bacteria 2 100.0 +k__Bacteria|p__Firmicutes 2|1239 72.20451 +k__Bacteria|p__Deferribacteres 2|200930 23.27657 +k__Bacteria|p__Bacteroidetes 2|976 4.51892 +k__Bacteria|p__Firmicutes|c__Clostridia 2|1239|186801 70.49728 +k__Bacteria|p__Deferribacteres|c__Deferribacteres 2|200930|68337 23.27657 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia 2|976|200643 4.51892 +k__Bacteria|p__Firmicutes|c__Firmicutes_unclassified 2|1239| 1.70723 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales 2|1239|186801|186802 70.49728 +k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales 2|200930|68337|191393 23.27657 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales 2|976|200643|171549 4.51892 +k__Bacteria|p__Firmicutes|c__Firmicutes_unclassified|o__Firmicutes_unclassified 2|1239|| 1.70723 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae 2|1239|186801|186802|31979 51.80893 +k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae 2|200930|68337|191393|191394 23.27657 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae 2|1239|186801|186802|186806 18.68835 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae 2|976|200643|171549|2005525 4.51892 +k__Bacteria|p__Firmicutes|c__Firmicutes_unclassified|o__Firmicutes_unclassified|f__Firmicutes_unclassified 2|1239||| 1.70723 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium 2|1239|186801|186802|31979|1485 51.80893 +k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Mucispirillum 2|200930|68337|191393|191394|248038 23.27657 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium 2|1239|186801|186802|186806|1730 18.68835 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides 2|976|200643|171549|2005525|375288 4.51892 +k__Bacteria|p__Firmicutes|c__Firmicutes_unclassified|o__Firmicutes_unclassified|f__Firmicutes_unclassified|g__Firmicutes_unclassified 2|1239|||| 1.70723 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium|s__Clostridium_sp_ASF502 2|1239|186801|186802|31979|1485|97139 37.0475 +k__Bacteria|p__Deferribacteres|c__Deferribacteres|o__Deferribacterales|f__Deferribacteraceae|g__Mucispirillum|s__Mucispirillum_schaedleri 2|200930|68337|191393|191394|248038|248039 23.27657 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Eubacteriaceae|g__Eubacterium|s__Eubacterium_plexicaudatum 2|1239|186801|186802|186806|1730|97253 18.68835 +k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium|s__Clostridium_sp_ASF356 2|1239|186801|186802|31979|1485|97138 14.76143 +k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides_goldsteinii 2|976|200643|171549|2005525|375288|328812 4.51892 k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Tannerellaceae|g__Parabacteroides|s__Parabacteroides_sp_ASF519 +k__Bacteria|p__Firmicutes|c__Firmicutes_unclassified|o__Firmicutes_unclassified|f__Firmicutes_unclassified|g__Firmicutes_unclassified|s__Firmicutes_bacterium_ASF500 2|1239|||||1378168 1.70723 diff --git a/tests/testthat/read_report/ref_output/metaphlan2-report-res.rds b/tests/testthat/read_report/ref_output/metaphlan2-report-res.rds new file mode 100644 index 0000000..3e61e4b Binary files /dev/null and b/tests/testthat/read_report/ref_output/metaphlan2-report-res.rds differ diff --git a/tests/testthat/read_report/ref_output/metaphlan3-report-res.rds b/tests/testthat/read_report/ref_output/metaphlan3-report-res.rds new file mode 100644 index 0000000..39ed71a Binary files /dev/null and b/tests/testthat/read_report/ref_output/metaphlan3-report-res.rds differ diff --git a/tests/testthat/test-read_report.R b/tests/testthat/test-read_report.R index 5ba41c4..dd86dfd 100644 --- a/tests/testthat/test-read_report.R +++ b/tests/testthat/test-read_report.R @@ -25,3 +25,19 @@ test_that("kraken2uniq input works", { expect_equal(res, readRDS("read_report/ref_output/k2uniq-report-res.rds")) }) +test_that("metaphlan2 input works", { + res <- read_report("read_report/input/metaphlan2-report.txt") + if (write_ref_output) + saveRDS(res, "read_report/ref_output/metaphlan2-report-res.rds") + + expect_equal(res, readRDS("read_report/ref_output/metaphlan2-report-res.rds")) +}) + + +test_that("metaphlan3 input works", { + res <- read_report("read_report/input/metaphlan3-report.txt") + if (write_ref_output) + saveRDS(res, "read_report/ref_output/metaphlan3-report-res.rds") + + expect_equal(res, readRDS("read_report/ref_output/metaphlan3-report-res.rds")) +})