Add support for MetaPhlAn3 reports (fixes #75)

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 = "[email protected]", role = c("aut", "cre"))

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 

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)) {

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
 

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

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	

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"))
+})