Commit 7e4d8611 authored by mcariou's avatar mcariou
Browse files

commit

parent 70125ace
......@@ -20,9 +20,12 @@ echo "--------------------------------------------------"
##################################################################################################################
module load R
echo "TMP version: blastdb from which sequences are retreived and taxo db used by Taxonomizer R package are written in the script, should be parameters"
BLASTDBNUC="~/2021_legio/blastdb/phyloref/phyloref_nuc"
TAXO="/home/mcariou/2021_legio/Taxo/accessionTaxa.sql
TAXO="/home/mcariou/2021_legio/Taxo/accessionTaxa.sql"
echo "~/2021_legio/blastdb/phyloref/phyloref_nuc"
echo "/home/mcariou/2021_legio/Taxo/accessionTaxa.sql"
# variable
OUT_BLAST=$1
......@@ -32,9 +35,7 @@ BLAST_REP=`echo $1 | awk -F "/" '{$NF=""; print $0}' | sed 's/ /\//g'`
FASTA_REP=$3
mkdir -p $FASTA_REP
#GENES=`grep ">" $4 | sed 's/>//g'`
GENES="lpg2300"
GENES=`grep ">" $4 | sed 's/>//g'`
EVAL=$5
PERCID=$6
......@@ -65,31 +66,11 @@ 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> $FASTA_REP/$Gene/paste_blast_test.log
Rscript --vanilla $rscript $subblast $EVAL $PERCID $PERCOVERLAP $NPERTAX $FASTA $BLASTDBNUC $TAXO > $FASTA_REP/$Gene/paste_blast_test.log
fi ;
# if [[ -s $subblast.mod ]] ; then
# echo "sp names already retrieved"
# else
# echo "debut de la boucle:"
# for id in `seq $nrow`
# do
# line=`sed -n ${id}p $subblast`
# idncbi=`sed -n ${id}p $subblast | awk '{print $3}' | awk -F[\.] '{print $1}'`
# tax=`efetch -db nuccore -id $idncbi -format docsum | xtract -pattern DocumentSummary -element Organism | sed 's/ /_/g'`
# echo $tax
# echo $line " " $tax >> $subblast.mod
# done
# fi ;
#if [[ -s $FASTA ]] ; then
#echo "sequences already retrieved"
#else
#echo "retrieve fasta"
#Rscript --vanilla $rscript $subblast.mod $EVAL $PERCID $PERCOVERLAP $NPERTAX $FASTA> $FASTA_REP/$Gene/paste_blast.log
#fi ;
done
......
......@@ -12,11 +12,11 @@
#$ -e /home/mcariou/2021_legio/log/
/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref/phyloref_prot ~/2021_legio/genes/78Lp_uniprot.fasta ~/2021_legio/out_blastn/
#/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref/phyloref_prot ~/2021_legio/genes/78Lp_uniprot.fasta ~/2021_legio/out_blastn/
## Doesn't accomodate multi query yet
#/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblastTMP.sh ~/2021_legio/out_blastn/78Lp_uniprot.psiblast ~/2021_legio/phylolegio/doc/tabAss.txt ~/2021_legio/fasta/lpg2300_50_50 ~/2021_legio/genes/lpg2300.fasta 0.0001 0.5 0.5 1
## IN TRIAL
/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/lpg2300_50_50 ~/2021_legio/genes/78Lp_uniprot.fasta 0.0001 0.5 0.5 1
# fin
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