From 33f7ac877c98c058a9d16e7fce970b6f6730fbff Mon Sep 17 00:00:00 2001
From: mcariou <115-mcariou@users.noreply.gitbio.ens-lyon.fr>
Date: Wed, 24 Nov 2021 18:26:56 +0100
Subject: [PATCH] script 5 in progress, cat
---
script/4_parse_PSIblast.R | 1 +
script/4_parse_PSIblast.sh | 1 -
script/5_cat_aln_phy.R | 47 +++++++++++++++++++++++++++++++++
script/5_cat_aln_phy.sh | 53 ++++++++++++++++++++++++++++++++++++++
script/test.log | 0
5 files changed, 101 insertions(+), 1 deletion(-)
create mode 100644 script/5_cat_aln_phy.R
create mode 100755 script/5_cat_aln_phy.sh
create mode 100644 script/test.log
diff --git a/script/4_parse_PSIblast.R b/script/4_parse_PSIblast.R
index ff2a5ad..b00f90f 100644
--- a/script/4_parse_PSIblast.R
+++ b/script/4_parse_PSIblast.R
@@ -101,6 +101,7 @@ system(cmd)
library(ape)
aln<-read.dna(fasta, format="fasta")
+aln<-clustal(aln)
names(listid_short)<-gsub(names(listid_short), pattern=" ", replacement="_")
diff --git a/script/4_parse_PSIblast.sh b/script/4_parse_PSIblast.sh
index 32b2b2b..cc81fa1 100755
--- a/script/4_parse_PSIblast.sh
+++ b/script/4_parse_PSIblast.sh
@@ -68,7 +68,6 @@ nrow=`cat $subblast | wc -l`
echo "sequences already retrieved"
else
echo "retrieve fasta"
- #Rscript --vanilla $rscript $subblast $EVAL $PERCID $PERCOVERLAP $NPERTAX $FASTA> $FASTA_REP/$Gene/paste_blast_test.log
Rscript --vanilla $rscript $subblast $EVAL $PERCID $PERCOVERLAP $NPERTAX $FASTA $BLASTDBNUC $TAXO > $FASTA_REP/$Gene/paste_blast_test.log
fi ;
diff --git a/script/5_cat_aln_phy.R b/script/5_cat_aln_phy.R
new file mode 100644
index 0000000..0de18aa
--- /dev/null
+++ b/script/5_cat_aln_phy.R
@@ -0,0 +1,47 @@
+#!/usr/bin/env Rscript
+args = commandArgs(trailingOnly=TRUE)
+
+# test if there is at least one argument: if not, return an error
+if (length(args)!=1) {
+ stop("1 arguments must be supplied.\n", call.=FALSE)
+}
+
+
+#args<-c("/home/mcariou/2021_legio/fasta/78Lp", "~/2020_Attaiech/prot_db/Transdecoder", "~/2021_legio/phylolegio/doc/tabAss.txt")
+#args<-c("/home/mcariou/2021_legio/fasta/78Lp")
+
+
+subrep<-list.files(args[1])
+subrep<-subrep[grep(x=subrep, pattern="Q5")]
+
+
+#### Change names in the fasta
+library(ape)
+
+
+cat<-list()
+
+
+#### fuction
+
+file<-list.files(paste0(args[1], "/", subrep[1]))
+file<-file[grep(x=file, pattern="aln")]
+aln<-read.dna(paste0(args[1], "/",subrep[1], "/", file), format="fasta", as.character=TRUE)
+
+tmp<-aln
+names(tmp)<-sapply(labels(aln), function(x) strsplit(x, split=".", fixed=TRUE)[[1]][1])
+
+for (seq in names(tmp)){
+ print(seq)
+ cat<-c(cat, list(seq=tmp[seq]))
+ names(cat)<-c(names(cat)[-length(cat)], seq)
+}
+
+
+
+#write.dna(aln, file=fasta_aln, format="fasta", nbcol = 6, colsep = "", colw = 10)
+
+
+
+
+
diff --git a/script/5_cat_aln_phy.sh b/script/5_cat_aln_phy.sh
new file mode 100755
index 0000000..3f47830
--- /dev/null
+++ b/script/5_cat_aln_phy.sh
@@ -0,0 +1,53 @@
+#!/bin/bash
+
+echo "USAGE: ./5_aln_phy.sh \$1=fasta_path"
+echo "--------------------------------------------------"
+
+
+##################################################################################################################
+### En local
+#./5_aln_phy.sh ~/Documents/CIRI_BIBS_projects/2021_04_Doublet/pipeline/fasta/ lp0952_ortho
+
+### PSMN
+#./5_cat_aln_phy.sh ~/2021_legio/fasta/78Lp/
+##################################################################################################################
+
+# variable
+DATA=$1
+FASTA=$1/concat.fasta
+PHYLIP=$1/concat.phylip
+
+echo $0
+rscript=`ls $0 | sed 's/.sh/.R/g'`
+echo $rscript
+
+
+
+if [[ -s $FASTA ]] ; then
+ echo "sequences already concatenated"
+else
+ echo "concatenate fasta"
+ Rscript --vanilla $rscript $DATA > $DATA/cat.log
+fi ;
+
+
+if [ -e $FASTA ] ; then
+ echo $FASTA" exists"
+
+ #prank -d=$FASTA +F -o=$ALN
+ echo $ALN
+ ## Convert to phylipX
+ trimal -in $FASTA -out $PHYLIP -phylip
+
+ ## phylogeny
+ phyml -i $PHYLIP -d nt -m HKY85 -a e -c 4 -s NNI -b -1
+
+else
+ echo $FASTA "do not exists. incorrect input"
+fi ;
+
+
+
+
+
+# fin
diff --git a/script/test.log b/script/test.log
new file mode 100644
index 0000000..e69de29
--
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