add legio strain in 4th script

script/4_parse_PSIblast.R

@@ -10,7 +10,7 @@ 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")
+#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", "~/2021_legio/blastdb/phyloref/phyloref_nuc", "/home/mcariou/2021_legio/Taxo/accessionTaxa.sql")
 
 
 print("reading arguments and data...")
@@ -75,22 +75,13 @@ print(paste0("Species names retrieved; dim blastn et taxa: ", dim(blastn), ", ",
 blastn<-cbind(blastn, Taxa)
 
 
-
-
-
-
-
-
-
-
-
-
-
-
-###############
+#########################
 # Here is time to keep legionella pneumophila strains
-##############
+##########################
+
+blastn_lp<-blastn[blastn$species=="Legionella pneumophila",]
 
+##########################
 
 
 #### Keep one sequence per subject id
@@ -111,13 +102,55 @@ blastn<-blastn[blastn$sseqid %in% listid,]
 print(paste("Keep best hit for each species, nrow = ", nrow(blastn)))
 
 listid_short<-sapply(listid, function(x) substr(x, 1, nchar(x)-2))
+
+
 #### Retrieve sequences via blastcmd
 system(paste0("rm ", fasta))
 for (seq in listid_short){ 
-cmd<-paste0("blastdbcmd -db ", blastdb, " -entry ",  seq, " >> ", fasta)
+cmd<-paste0("blastdbcmd -db ", blastdb, " -entry ",  seq, " >> ", fasta, "_L")
 system(cmd)
 }
 
+listid_short_L<-listid_short
+
+#################################################################################################
+### Legionella pneumophila
+blastn_lp$evalue<-unlist(blastn_lp$evalue)
+blastn_lp$length<-unlist(blastn_lp$length)
+blastn_lp$sseqid<-unlist(blastn_lp$sseqid)
+
+listid<-blastn_lp$sseqid
+
+print(paste("Keep best hit for each species, nrow = ", nrow(blastn_lp)))
+
+listid_short<-sapply(listid, function(x) substr(x, 1, nchar(x)-2))
+
+
+#### Retrieve sequences via blastcmd
+for (seq in listid_short){
+cmd<-paste0("blastdbcmd -db ", blastdb, " -entry ",  seq, " >> ", fasta, "_lp")
+system(cmd)
+}
+
+listid_short_lp<-listid_short
+#### And cat
+
+cmd<-paste0("cat ", fasta, "_L ", fasta, "_lp > ", fasta)
+system(cmd)
+
+
+###########################################################################
+
+
+
+
+
+
+
+
+
+
+##################################################################################################
 
 #### Change names in the fasta
 library(ape)
@@ -125,6 +158,18 @@ library(ape)
 aln<-read.dna(fasta, format="fasta")
 alnaln<-clustal(aln)
 
+
+
+
+
+
+
+names(listid_short_lp)<-paste0("Legionella pneumophila.", names(listid_short_lp))
+
+listid_short<-c(listid_short_L, listid_short_lp)
+
+
+
 #names(alnaln)<-names(aln)
 
 names(listid_short)<-gsub(names(listid_short), pattern=" ", replacement="_")
@@ -133,7 +178,7 @@ tmp<-sapply(rownames(alnaln), function(x) strsplit(x, " ")[[1]][1])
 
 
 newnames<-sapply(tmp, function(x){
- names(listid_short)[listid_short==x]
+ names(listid_short)[listid_short==x][1]
 })
 
 rownames(alnaln)<-newnames

script/psmn/runscript_78Lp_step34.sh

@@ -16,7 +16,7 @@ module load trimal
 
 
 
-#/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblast.sh  ~/2021_legio/out_blastn/78Lp_uniprot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/78Lp ~/2021_legio/genes/78Lp_uniprot.fasta 0.0001 0.5 0.5 1
+/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblast.sh  ~/2021_legio/out_blastn/78Lp_uniprot.psiblast  ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/78Lp ~/2021_legio/genes/78Lp_uniprot.fasta 0.0001 0.5 0.5 1
 
 
 /home/mcariou/2021_legio/phylolegio/script/5_cat_aln_phy.sh ~/2021_legio/fasta/78Lp/