--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gentest.R	Fri Nov 08 18:52:17 2019 -0500
@@ -0,0 +1,99 @@
+library(dada2, quietly=T)
+library(ggplot2, quietly=T)
+
+fwd <- c('F3D0_S188_L001_R1_001.fastq.gz')
+rev <- c('F3D0_S188_L001_R2_001.fastq.gz')
+
+sample.names <- c('F3D0_S188_L001')
+
+names(fwd) <- sample.names
+names(rev) <- sample.names
+
+
+filt.fwd <- c('filterAndTrim_F3D0_R1.fq.gz')
+filt.rev <- c('filterAndTrim_F3D0_R2.fq.gz')
+
+ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev)
+
+# In the test no name can be given to the collection
+rownames(ftout) <- c( 'Unnamed Collection' )
+write.table(ftout, "filterAndTrim_F3D0.tab", quote=F, sep="\t", col.names=NA)
+
+# Plot quality profile (just for one file, Galaxy compares with sim_size)
+
+qp <- plotQualityProfile(fwd)
+ggsave('qualityProfile.pdf', qp, width = 20,height = 15,units = c("cm"))
+
+# Plot complexity (just for one file, Galaxy compares with sim_size)
+
+cp <- plotComplexity(fwd)
+ggsave('complexity.pdf', cp, width = 20,height = 15,units = c("cm"))
+
+
+# learn Errors
+err.fwd <- learnErrors(filt.fwd) 
+saveRDS(err.fwd, file='learnErrors_F3D0_R1.Rdata')
+plot <- plotErrors(err.fwd)
+ggsave('learnErrors_F3D0_R1.pdf', plot, width = 20,height = 15,units = c("cm"))
+
+err.rev <- learnErrors(filt.fwd) 
+saveRDS(err.rev, file='learnErrors_F3D0_R2.Rdata')
+plot <- plotErrors(err.rev)
+ggsave('learnErrors_F3D0_R2.pdf', plot, width = 20,height = 15,units = c("cm"))
+
+# dada 
+dada.fwd <- dada(filt.fwd, err.fwd)
+saveRDS(dada.fwd, file="dada_F3D0_R1.Rdata")
+dada.rev <- dada(filt.rev, err.rev)
+saveRDS(dada.rev, file="dada_F3D0_R2.Rdata")
+
+# merge pairs
+merged <- mergePairs(dada.fwd, filt.fwd, dada.rev, filt.rev)
+saveRDS(merged, file='mergePairs_F3D0.Rdata')
+
+# make sequence table
+seqtab <- makeSequenceTable(merged)
+write.table(t(seqtab), file="makeSequenceTable_F3D0.tab", quote=F, sep="\t", row.names = T, col.names = NA)
+
+reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
+df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)
+pdf( 'makeSequenceTable_F3D0.pdf' )
+ggplot(data=df, aes(x=length, y=count)) +
+    geom_col() +
+    theme_bw()
+bequiet <- dev.off()
+
+# remove bimera
+seqtab.nochim <- removeBimeraDenovo(seqtab)
+write.table(t(seqtab), file="removeBimeraDenovo_F3D0.tab", quote=F, sep="\t", row.names = T, col.names = NA)
+
+# assign taxonomy/species
+tl <- 'Level1,Level2,Level3,Level4,Level5'
+tl <- strsplit(tl, ",")[[1]]
+
+taxa <- assignTaxonomy(seqtab.nochim, 'reference.fa', outputBootstraps = T, taxLevels=c('Level1','Level2','Level3','Level4','Level5'))
+
+taxa$tax <- addSpecies(taxa$tax, 'reference_species.fa')
+write.table(taxa$tax, file = 'assignTaxonomyAddspecies_F3D0.tab', quote = F, sep = "\t", row.names = T, col.names = NA)
+
+write.table(taxa$boot, file = 'assignTaxonomyAddspecies_F3D0_boot.tab', quote = F, sep = "\t", row.names = T, col.names = NA)
+
+
+
+## Generate extra test data for parameter testing 
+
+filterAndTrim(fwd, c('filterAndTrim_single_F3D0_R1.fq.gz'), rm.phix = T, orient.fwd = 'TACGG')
+
+filterAndTrim(fwd, c('filterAndTrim_single_trimmers_F3D0_R1.fq.gz'), truncQ = 30, truncLen = 2, trimLeft = 150, trimRight = 2)
+
+filterAndTrim(fwd, c('filterAndTrim_single_filters_F3D0_R1.fq.gz'), maxLen = 255, minLen = 60, maxN = 100, minQ = 13, maxEE = 1)
+
+
+merged_nondef <- mergePairs(dada.fwd, filt.fwd, dada.rev, filt.rev, minOverlap = 8, maxMismatch = 1, justConcatenate = TRUE, trimOverhang = TRUE)
+saveRDS(merged_nondef, file='mergePairs_F3D0_nondefault.Rdata')
+
+rb.dada.fwd <- removeBimeraDenovo(dada.fwd)
+write.table(rb.dada.fwd, file = 'removeBimeraDenovo_F3D0_dada_uniques.tab', quote = F, sep = "\t", row.names = T, col.names = F)
+
+rb.merged <- removeBimeraDenovo(merged, method="pooled")
+saveRDS(rb.merged, file='removeBimeraDenovo_F3D0_mergepairs.Rdata')