add species

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

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!"
 

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"
 
 

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