From d6951de0259467307a50ca93ba41b0c294eaf578 Mon Sep 17 00:00:00 2001
From: amos <raphenar@mcmaster.ca>
Date: Fri, 8 Sep 2023 16:02:51 -0400
Subject: [PATCH] use load command

---
 test.sh | 129 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 65 insertions(+), 64 deletions(-)

diff --git a/test.sh b/test.sh
index 362dde1..fb1ca46 100755
--- a/test.sh
+++ b/test.sh
@@ -22,70 +22,71 @@ echo "=================================== RGI EXECUTABLE LOCATION ==============
 which rgi
 rgi -h
 
-echo "=================================== RGI AUTO LOAD ==================================="
-rgi auto_load --clean
-# echo "=================================== DOWNLOAD CARD CANONICAL DATA ==================================="
-# # get latest card database
-# wget -O card_data.tar.bz2 --no-check-certificate https://card.mcmaster.ca/latest/data
-# mkdir -p card_data
-# tar xf card_data.tar.bz2 -C card_data
-#
-# echo "=================================== DOWNLOAD CARD VARIANTS DATA ==================================="
-# # get latest card variants
-# wget -O prevalence-v4.0.0.tar.bz2 --no-check-certificate https://card.mcmaster.ca/download/6/prevalence-v4.0.0.tar.bz2
-# mkdir -p card_variants
-# tar xf prevalence-v4.0.0.tar.bz2 -C card_variants
-# gunzip card_variants/*.gz
-#
-# echo "=================================== CARD CANONICAL ANNOTATIONS ==================================="
-# # create fasta files with annotations from card.json
-# echo "$cmd rgi card_annotation --input card_data/card.json"
-# rgi card_annotation --input card_data/card.json
-#
-# echo "=================================== VERSIONS ==================================="
-# # remove file with '_all.fasta'
-# rm card_database_v*_all.fasta
-# data_version=`echo card_database_v*.fasta | sed 's/.*card_database_v\(.*\).fasta/\1/'`
-# echo "$cmd data_version: $data_version"
-# variants_version=`echo prevalence-v*.tar.bz2 | sed 's/.*prevalence-v\(.*\).tar.bz2/\1/'`
-# echo "$cmd variants_version: $variants_version"
-#
-# echo "=================================== CARD VARIANTS ANNOTATIONS ==================================="
-# # create fasta files with annotations from variants
-# echo "$cmd rgi wildcard_annotation --input_directory card_variants --version '$variants_version' --card_json card_data/card.json"
-# rgi wildcard_annotation --input_directory card_variants --version "$variants_version" --card_json card_data/card.json
-#
-# echo "=================================== CLEAN OLD DATABASES ==================================="
-# # clean
-# echo "$cmd rgi clean --debug"
-# rgi clean --debug
-#
-# echo "=================================== LOAD DATABASES ==================================="
-# # load
-# echo "$cmd rgi load --card_json card_data/card.json --card_annotation card_database_v${data_version}.fasta --wildcard_index card_variants/index-for-model-sequences.txt --wildcard_version '$variants_version' --wildcard_annotation wildcard_database_v${variants_version}.fasta --debug"
-# rgi load --card_json card_data/card.json --card_annotation card_database_v${data_version}.fasta --wildcard_index card_variants/index-for-model-sequences.txt --wildcard_version "$variants_version" --wildcard_annotation wildcard_database_v${variants_version}.fasta --debug
-#
-#
-# echo "=================================== CHECK LOADED DATABASES ==================================="
-# # check database
-# echo "$cmd rgi database -v --all"
-# rgi database -v --all
-#
-# echo "=================================== COPY DATA & INPUTS ==================================="
-# # for test_1.py
-# echo "$cmd cp card_data/card.json app/_data"
-# cp card_data/card.json app/_data
-#
-# # for test_3.py
-# echo "$cmd cp card_data/card.json tests/inputs"
-# cp card_data/card.json tests/inputs
-#
-# echo "=================================== CLEAN ==================================="
-#
-# # clean up files
-# rm -r card_*
-# rm wildcard_database_v*
-# rm prevalence-v*
+# echo "=================================== RGI AUTO LOAD ==================================="
+# rgi auto_load --clean
+
+echo "=================================== DOWNLOAD CARD CANONICAL DATA ==================================="
+# get latest card database
+wget --quiet -O card_data.tar.bz2 --no-check-certificate https://card.mcmaster.ca/latest/data
+mkdir -p card_data
+tar xf card_data.tar.bz2 -C card_data
+
+echo "=================================== DOWNLOAD CARD VARIANTS DATA ==================================="
+# get latest card variants
+wget --quiet -O prevalence-v4.0.0.tar.bz2 --no-check-certificate https://card.mcmaster.ca/download/6/prevalence-v4.0.0.tar.bz2
+mkdir -p card_variants
+tar xf prevalence-v4.0.0.tar.bz2 -C card_variants
+gunzip card_variants/*.gz
+
+echo "=================================== CARD CANONICAL ANNOTATIONS ==================================="
+# create fasta files with annotations from card.json
+echo "$cmd rgi card_annotation --input card_data/card.json"
+python3 ./rgi card_annotation --input card_data/card.json
+
+echo "=================================== VERSIONS ==================================="
+# remove file with '_all.fasta'
+rm card_database_v*_all.fasta
+data_version=`echo card_database_v*.fasta | sed 's/.*card_database_v\(.*\).fasta/\1/'`
+echo "$cmd data_version: $data_version"
+variants_version=`echo prevalence-v*.tar.bz2 | sed 's/.*prevalence-v\(.*\).tar.bz2/\1/'`
+echo "$cmd variants_version: $variants_version"
+
+echo "=================================== CARD VARIANTS ANNOTATIONS ==================================="
+# create fasta files with annotations from variants
+echo "$cmd rgi wildcard_annotation --input_directory card_variants --version '$variants_version' --card_json card_data/card.json"
+python3 ./rgi wildcard_annotation --input_directory card_variants --version "$variants_version" --card_json card_data/card.json
+
+echo "=================================== CLEAN OLD DATABASES ==================================="
+# clean
+echo "$cmd rgi clean --debug"
+python3 ./rgi clean --debug
+
+echo "=================================== LOAD DATABASES ==================================="
+# load
+echo "$cmd rgi load --card_json card_data/card.json --card_annotation card_database_v${data_version}.fasta --wildcard_index card_variants/index-for-model-sequences.txt --wildcard_version '$variants_version' --wildcard_annotation wildcard_database_v${variants_version}.fasta --debug"
+python3 ./rgi load --card_json card_data/card.json --card_annotation card_database_v${data_version}.fasta --wildcard_index card_variants/index-for-model-sequences.txt --wildcard_version "$variants_version" --wildcard_annotation wildcard_database_v${variants_version}.fasta --debug
+
+
+echo "=================================== CHECK LOADED DATABASES ==================================="
+# check database
+echo "$cmd rgi database -v --all"
+python3 ./rgi database -v --all
+
+echo "=================================== COPY DATA & INPUTS ==================================="
+# for test_1.py
+echo "$cmd cp card_data/card.json app/_data"
+cp card_data/card.json app/_data
+
+# for test_3.py
+echo "$cmd cp card_data/card.json tests/inputs"
+cp card_data/card.json tests/inputs
+
+echo "=================================== CLEAN ==================================="
+
+# clean up files
+rm -r card_*
+rm wildcard_database_v*
+rm prevalence-v*
 
 echo "=================================== RUN TESTS ==================================="
 # run unit tests