From f7322c7a79fb096d4f3c2efb283af6a2e99073d4 Mon Sep 17 00:00:00 2001
From: amos <raphenar@mcmaster.ca>
Date: Thu, 7 Sep 2023 15:05:31 -0400
Subject: [PATCH] use rgi auto load

---
 test.sh | 126 ++++++++++++++++++++++++++++----------------------------
 1 file changed, 64 insertions(+), 62 deletions(-)

diff --git a/test.sh b/test.sh
index 4f6c562..35ec5bd 100755
--- a/test.sh
+++ b/test.sh
@@ -22,68 +22,70 @@ echo "=================================== RGI EXECUTABLE LOCATION ==============
 which rgi
 rgi -h
 
-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 "$cmd cp card_data/card.json tests/inputs"
-cp card_data/card.json tests/inputs
-
-echo "=================================== CLEAN ==================================="
-
-# clean up files
-rm -r card_*
-rm wildcard_database_v*
-rm prevalence-v*
+echo "=================================== RGI AUTO LOAD ==================================="
+rgi auto_load --clean --debug
+# echo "=================================== DOWNLOAD CARD CANONICAL DATA ==================================="
+# # get latest card database
+# wget -O card_data.tar.bz2 --no-check-certificate https://card.mcmaster.ca/latest/data
+# mkdir -p card_data
+# tar xf card_data.tar.bz2 -C card_data
+#
+# echo "=================================== DOWNLOAD CARD VARIANTS DATA ==================================="
+# # get latest card variants
+# wget -O prevalence-v4.0.0.tar.bz2 --no-check-certificate https://card.mcmaster.ca/download/6/prevalence-v4.0.0.tar.bz2
+# mkdir -p card_variants
+# tar xf prevalence-v4.0.0.tar.bz2 -C card_variants
+# gunzip card_variants/*.gz
+#
+# echo "=================================== CARD CANONICAL ANNOTATIONS ==================================="
+# # create fasta files with annotations from card.json
+# echo "$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 "=================================== RUN TESTS ==================================="
 # run unit tests