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Fix arguments and paths for make_msa.sh, make make_ss.sh executable

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alephreish 2024-10-22 12:28:56 +03:00
parent 6c8514053a
commit 0b87de00c7
3 changed files with 12 additions and 5 deletions
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0
input_prep/make_ss.sh Normal file → Executable file
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13
make_msa.sh
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@ -8,16 +8,23 @@ out_dir="$2"
CPU="$3" CPU="$3"
MEM="$4" MEM="$4"
# directory with the databases
SEARCH_BASE="$5"
# template database # template database
DB_TEMPL="$5" DB_TEMPL="$6"
# current script directory (i.e., pipe directory) # current script directory (i.e., pipe directory)
SCRIPT=`realpath -s $0` SCRIPT=`realpath -s $0`
export PIPE_DIR=`dirname $SCRIPT` export PIPE_DIR=`dirname $SCRIPT`
if [ -z "$SEARCH_BASE" ]; then
SEARCH_BASE=$PIPE_DIR
fi
# sequence databases # sequence databases
DB_UR30="$PIPE_DIR/UniRef30_2020_06/UniRef30_2020_06" DB_UR30="$SEARCH_BASE/UniRef30_2020_06/UniRef30_2020_06"
DB_BFD="$PIPE_DIR/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt" DB_BFD="$SEARCH_BASE/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt"
# Running signalP 6.0 # Running signalP 6.0
mkdir -p $out_dir/signalp mkdir -p $out_dir/signalp

4
rf2aa/data/preprocessing.py
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@ -28,8 +28,8 @@ def make_msa(
if out_a3m.exists() and out_atab.exists() and out_hhr.exists(): if out_a3m.exists() and out_atab.exists() and out_hhr.exists():
return out_a3m, out_hhr, out_atab 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) print(search_command)
_ = subprocess.run(search_command, shell=True) _ = subprocess.run(search_command)
return out_a3m, out_hhr, out_atab return out_a3m, out_hhr, out_atab