From e62c21ec714782fcc6ac444828ed957a4b033311 Mon Sep 17 00:00:00 2001
From: alephreish <alephreish@gmail.com>
Date: Tue, 22 Oct 2024 12:28:56 +0300
Subject: [PATCH] Fix arguments and paths for make_msa.sh

---
 make_msa.sh                 | 13 ++++++++++---
 rf2aa/data/preprocessing.py |  4 ++--
 2 files changed, 12 insertions(+), 5 deletions(-)

diff --git a/make_msa.sh b/make_msa.sh
index 4a3c98c..2ab1a9f 100755
--- a/make_msa.sh
+++ b/make_msa.sh
@@ -8,16 +8,23 @@ out_dir="$2"
 CPU="$3"
 MEM="$4"
 
+# directory with the databases
+SEARCH_BASE="$5"
+
 # template database
-DB_TEMPL="$5"
+DB_TEMPL="$6"
 
 # current script directory (i.e., pipe directory)
 SCRIPT=`realpath -s $0`
 export PIPE_DIR=`dirname $SCRIPT`
 
+if [ -z "$SEARCH_BASE" ]; then
+    SEARCH_BASE=$PIPE_DIR
+fi
+
 # sequence databases
-DB_UR30="$PIPE_DIR/UniRef30_2020_06/UniRef30_2020_06"
-DB_BFD="$PIPE_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
+DB_UR30="$SEARCH_BASE/UniRef30_2020_06/UniRef30_2020_06"
+DB_BFD="$SEARCH_BASE/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
 
 # Running signalP 6.0
 mkdir -p $out_dir/signalp
diff --git a/rf2aa/data/preprocessing.py b/rf2aa/data/preprocessing.py
index 8624d55..9a363fc 100644
--- a/rf2aa/data/preprocessing.py
+++ b/rf2aa/data/preprocessing.py
@@ -28,8 +28,8 @@ def make_msa(
     if out_a3m.exists() and out_atab.exists() and out_hhr.exists():
         return out_a3m, out_hhr, out_atab
 
-    search_command = f"./{command} {fasta_file} {out_dir} {num_cpus} {ram_gb} {search_base} {template_database}"
+    search_command = list(map(str, [ command, fasta_file, out_dir, num_cpus, ram_gb, search_base, template_database ]))
     print(search_command)
-    _ = subprocess.run(search_command, shell=True)
+    _ = subprocess.run(search_command)
     return out_a3m, out_hhr, out_atab