Commit 15a080aa authored by mcariou's avatar mcariou
Browse files

update

parent 72879ec6
......@@ -10,6 +10,8 @@ if (length(args)!=8) {
#args<-c("/home/mcariou/2021_legio/fasta/78Lp/Q5ZXP3_lpg0688/Q5ZXP3_lpg0688.psiblast", "0.0001", "0.3", "0.5", "1", "/home/mcariou/2021_legio/fasta/78Lp/Q5ZXP3_lpg0688/Q5ZXP3_lpg0688.fasta")
#args<-c("/home/mcariou/2021_legio/out_blastn/lpg2300.psiblast", "0.0001", "0.1", "0.1", "1", "/home/mcariou/2021_legio/fasta/lpg2300/lpg2300.fasta", "~/2021_legio/blastdb/phyloref/phyloref_nuc", "/home/mcariou/2021_legio/Taxo/accessionTaxa.sql")
#args<-c("/home/adminmarie/Documents/CIRI_BIBS_projects/2021_04_Doublet/pipeline/fasta/78Lp/Q5ZXP3_lpg0688/Q5ZXP3_lpg0688.psiblast", "0.0001", "0.3", "0.5", "1", "/home/mcariou/2021_legio/fasta/78Lp/Q5ZXP3_lpg0688/Q5ZXP3_lpg0688.fasta")
print("reading arguments and data...")
......@@ -72,6 +74,25 @@ print(paste0("Species names retrieved; dim blastn et taxa: ", dim(blastn), ", ",
blastn<-cbind(blastn, Taxa)
###############
# Here is time to keep legionella pneumophila strains
##############
#### Keep one sequence per subject id
selecthit<-function(species){
tmp<-blastn[blastn$specie==species,]
......
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