Commit 6c4b2490 authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Generate new table

parent defb4688
#!/bin/R
require(plyr)
load("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/HMP_IGC_mapping/HMP_IGC_mapping.Rdat")
prodigal.dat <- read.table("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/prodigal_analysis/prodigal_summary.tsv", header=T)
all.dat.3$Assembly <- mapvalues(all.dat.3$Assembly, from = c("MetAmos_MG", "MetAmos_MGMT"),
to = c("MetAMOS_MG", "MetAMOS_MGMT")
all.dat.3$Assembly <- mapvalues(all.dat.3$Assembly, from = c("MetAmos_MG", "MetAmos_MGMT", "IMP_IGC"),
to = c("MetAMOS_MG", "MetAMOS_MGMT", "IGC_mapping")
)
all.dat.4 <- merge(all.dat.3, prodigal.dat, by=c("Dataset", "Assembly"), all.y=F)
all.dat.4 <- merge(all.dat.3, prodigal.dat, by=c("Dataset", "Assembly"), all=T)
all.dat.4 <- all.dat.4[-which(all.dat.4$Assembly%in%c("MetAMOS_MT", "MOCAT_MT",
"MetAmos_IGC", "MOCAT_IGC")),]
all.dat.4 <- all.dat.4[-which(all.dat.4$Assembly=="IMP_MT"),]
write.table(all.dat.4, "/home/shaman/Documents/Publications/IMP-manuscript/tables/second_iteration/all_comparison-v4.tsv", sep="\t", quote=F, row.names=F)
write.table(all.dat.4, "/home/shaman/Documents/Publications/IMP-manuscript/tables/second_iteration/all_comparison-v5.tsv", sep="\t", quote=F, row.names=F)
#save.image("/home/shaman/Work/Data/integrated-omics-pipeline/MS_analysis/prodigal_analysis/prodigal_analyses.Rdat")
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