From 6761d888fb8ccbe5127b9ba906384e1fb63faa15 Mon Sep 17 00:00:00 2001
From: Vyacheslav Brover <vyacheslav.brover@nih.gov>
Date: Fri, 14 Feb 2025 10:03:57 -0500
Subject: [PATCH] #3 --> #3 and #4

---
 genetics/tblastn.sh | 25 ++++++++++++++-----------
 1 file changed, 14 insertions(+), 11 deletions(-)

diff --git a/genetics/tblastn.sh b/genetics/tblastn.sh
index 4557c4a2..b9ba18f4 100755
--- a/genetics/tblastn.sh
+++ b/genetics/tblastn.sh
@@ -1,22 +1,24 @@
 #!/bin/bash --noprofile
 THIS=$( dirname $0 )
 source $THIS/../bash_common.sh
-if [ $# -ne 6 ]; then
+if [ $# -ne 7 ]; then
   echo "Run tblastn"
   echo "#1: query protein FASTA file"
   echo "#2: subject nucleotide FASTA file, may be gzip'ped"
-  echo "#3: tblastn parameters (except: -query -subject -db -out)"
-  echo "#4: part_size"
-  echo "#5: cores"
-  echo "#6: output file"
+  echo "#3: tblastn search parameters (except: -query -subject -db -out -outfmt)"
+  echo "#4: tblastn output parameters (-outfmt 6 ...)"
+  echo "#5: part_size"
+  echo "#6: cores"
+  echo "#7: output file"
   exit 1
 fi
 PROT=$1
 DNA=$2
-PARM=$3
-PART=$4  # 50000000 ??
-CORES=$5
-OUT=$6
+SEARCH=$3
+OUTFMT=$4
+PART=$5
+CORES=$6
+OUT=$7
 
 
 TMP=$( mktemp )
@@ -28,9 +30,10 @@ if [ -z ${DNA##*.gz} ]; then
   DNA=$TMP
 fi
 mkdir $TMP.dna
-$THIS/splitFasta $DNA $TMP.dna -group_size $PART
+# PAR
+$THIS/splitFasta $DNA $TMP.dna  -group_size $PART  -mono_nuc_max 20
 mkdir $TMP.out
-$THIS/../trav $TMP.dna  -step 1  -threads $CORES  "tblastn  -query $PROT  -subject %d/%f  $PARM  > $TMP.out/%f" 
+$THIS/../trav $TMP.dna  -step 1  -threads $CORES  "tblastn  -query $PROT  -subject %d/%f  $SEARCH  -outfmt '6 $OUTFMT' > $TMP.out/%f" 
 #tblastn  -query $PROT  -subject $DNA  -comp_based_stats 0  -evalue 1e-10  -seg no  -max_target_seqs 10000  -task tblastn-fast  -threshold 100  -window_size 15  -db_gencode 11  -outfmt '6 sseqid qseqid sstart send slen qstart qend qlen nident length'
 #                                                                                                                                                                                           1      2      3      4    5    6      7    8    9      10
 $THIS/../trav $TMP.out "cat %d/%f" > $OUT