Commit 5a8bf2b1 authored by mcariou's avatar mcariou
Browse files

V2

parent e971674a
......@@ -20,11 +20,11 @@ module purge
HOME="/home/mcariou/2021_legio/"
OUT=$HOME"blastdb/phyloref/"
OUT=$HOME"blastdb/phyloref_V2/"
CAT=$OUT"/cat_phyloref_cds.fasta"
CATPROT=$OUT"/cat_phyloref_pep.fasta"
Trans="/home/mcariou/2020_Attaiech/prot_db/Transdecoder/"
TAB=$HOME"/phylolegio/doc/tabAss.txt"
TAB=$HOME"/phylolegio/doc/tabAss_V2.txt"
mkdir -p $OUT
......@@ -34,14 +34,14 @@ mkdir -p $OUT
if [[ -s $CAT ]] ; then
echo "cat already exists"
else
for genome in `cat $TAB | sed '1d'| awk '{print $1}'`
for genome in `cat $TAB | sed '1d'| awk -F ";" '{print $1}'`
do
file=${Trans}/${genome}*/longest_orfs.cds
file2=`echo $file`
if [[ -s $file2 ]] ; then
cat $file2 >> $CAT
else
echo "doesn't: $file2"
echo "doesn't: $file"
fi
done
fi
......
#!/bin/bash
#$ -S /bin/bash
## name of the job to follow them
#$ -N runscript_V2
## name of the queue to be used
#$ -q E5-2670deb*,E5-2667v2*,E5-2667v4*
#$ -cwd
#$ -V
## where to put the log files (output and error) automatically generated by the cluster (different from the .log generated by DGINN)
## the dirs must exist before job is launched
#$ -o /home/mcariou/2021_legio/log/
#$ -e /home/mcariou/2021_legio/log/
module load trimal
/home/mcariou/2021_legio/phylolegio/script/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref_V2/phyloref_prot ~/2021_legio/genes/78Lp_uniprot.fasta ~/2021_legio/out_blastn/
/home/mcariou/2021_legio/phylolegio/script/4_parse_PSIblast.sh ~/2021_legio/out_blastn/78Lp_uniprot_V2.psiblast ~/2021_legio/phylolegio/doc/tabAss_V2.txt ~/2021_legio/fasta/78Lp_V2 ~/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_V2/
# fin
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