Commit aff74e46 authored by mcariou's avatar mcariou
Browse files

add species

parent 6be68d94
......@@ -53,7 +53,7 @@ fi
### Make Blast db
#makeblastdb -dbtype nucl -in $CAT -hash_index -out $OUT/phyloref_nuc -parse_seqids
makeblastdb -dbtype nucl -in $CAT -hash_index -out $OUT/phyloref_nuc -parse_seqids
###
# need to translate
transeq -sequence $CAT -outseq $CATPROT
......
......@@ -58,8 +58,8 @@ echo $REP_OUT
psiblast -db $REP_DB -query ${gene}.fasta -evalue 10 \
-outfmt "7 qseqid qlen sseqid slen length pident evalue nident mismatch gapopen qstart qend qseq bitscrore score sstart send sseq sstrand" \
-out $REP_OUT/${gene_name}.psiblast -max_target_seqs 5000 \
-num_iterations 0 -out_pssm $REP_OUT/log
-out $REP_OUT/${gene_name}.psiblast -max_target_seqs 500 \
-num_iterations 4 -out_pssm $REP_OUT/log
echo "program done!"
......@@ -21,9 +21,9 @@ 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"
BLASTDBNUC="~/2021_legio/blastdb/phyloref_V2/phyloref_nuc"
TAXO="/home/mcariou/2021_legio/Taxo/accessionTaxa.sql"
echo "~/2021_legio/blastdb/phyloref/phyloref_nuc"
echo "~/2021_legio/blastdb/phyloref_V2/phyloref_nuc"
echo "/home/mcariou/2021_legio/Taxo/accessionTaxa.sql"
......
......@@ -15,14 +15,15 @@ module load trimal
#/home/mcariou/2021_legio/phylolegio/script/2_make_db.sh /home/mcariou/2021_legio/doc/tabAss_V2.txt /home/mcariou/2020_Attaiech/prot_db/Transdecoder/ /home/mcariou/2021_legio/blastdb/phyloref_V2
/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/3_make_PSIblast.sh ~/2021_legio/blastdb/phyloref_V2/phyloref_prot ~/2021_legio/genes/78Lp_uniprot.fasta ~/2021_legio/out_blastn/
#mv ~/2021_legio/out_blastn/78Lp_uniprot.psiblast ~/2021_legio/out_blastn/78Lp_uniprot_V2.psiblast
#/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/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/
/home/mcariou/2021_legio/phylolegio/script/5_cat_aln_phy.sh ~/2021_legio/fasta/78Lp_V2/
# fin
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