From aff74e46844f182d3bfb06c07cccccd24c7d93ac Mon Sep 17 00:00:00 2001
From: mcariou <115-mcariou@users.noreply.gitbio.ens-lyon.fr>
Date: Tue, 25 Jan 2022 09:37:04 +0100
Subject: [PATCH] add species
---
script/2_make_db.sh | 2 +-
script/3_make_PSIblast.sh | 4 ++--
script/4_parse_PSIblast.sh | 4 ++--
script/psmn/runscript_78Lp_V2.sh | 7 ++++---
4 files changed, 9 insertions(+), 8 deletions(-)
diff --git a/script/2_make_db.sh b/script/2_make_db.sh
index c1ea9dc..bdda96e 100755
--- a/script/2_make_db.sh
+++ b/script/2_make_db.sh
@@ -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
diff --git a/script/3_make_PSIblast.sh b/script/3_make_PSIblast.sh
index 18665bd..0a17d94 100755
--- a/script/3_make_PSIblast.sh
+++ b/script/3_make_PSIblast.sh
@@ -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!"
diff --git a/script/4_parse_PSIblast.sh b/script/4_parse_PSIblast.sh
index cc81fa1..052c891 100755
--- a/script/4_parse_PSIblast.sh
+++ b/script/4_parse_PSIblast.sh
@@ -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"
diff --git a/script/psmn/runscript_78Lp_V2.sh b/script/psmn/runscript_78Lp_V2.sh
index a6843e7..ed52de7 100755
--- a/script/psmn/runscript_78Lp_V2.sh
+++ b/script/psmn/runscript_78Lp_V2.sh
@@ -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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