Merge pull request #28 from biomedbigdata/eqtl_mapping

added eqtl mapping to e2e

.dockerignore

@@ -13,6 +13,7 @@ cmake-*
 data/**
 !data/dbSNP
 !data/BIOGRID
+!data/eqtl_mapping
 
 # .DS_Store files
 *.DS_Store

docker/NeEDL/Dockerfile

@@ -53,6 +53,7 @@ COPY quepistasis ./quepistasis
 # copy files in /data
 COPY data/dbSNP/inc_pseudogenes /NeEDL/data/dbSNP/inc_pseudogenes
 COPY data/BIOGRID /NeEDL/data/BIOGRID
+COPY data/eqtl_mapping /NeEDL/data/eqtl_mapping
 
 # initialize everything needed for the build and build all targets
 RUN python3.10 install.py --clean --skip-vcpkg-setup --system-boost && \ 
@@ -81,6 +82,7 @@ RUN apt-get update -y && apt-get install -y python3.10 python3.10-dev sqlite3 g+
 COPY --from=build /NeEDL/test/model/bin/* /NeEDL/test/model/bin/
 COPY --from=build /NeEDL/data/dbSNP/inc_pseudogenes/snps_restruc_full_inc_pseudo.csv /NeEDL/data/dbSNP/inc_pseudogenes/snps_restruc_full_inc_pseudo.csv
 COPY --from=build /NeEDL/data/BIOGRID/BIOGRID-ORGANISM-Homo_sapiens-3.5.182.tab2.txt /NeEDL/data/BIOGRID/BIOGRID-ORGANISM-Homo_sapiens-current.tab2.txt
+COPY --from=build /NeEDL/data/eqtl_mapping/eqtl_mapping.csv /NeEDL/data/eqtl_mapping/eqtl_mapping.csv
 COPY --from=build /NeEDL/ext/plink/plink_linux_x86_64_20230116/ /NeEDL/ext/plink/plink_linux_x86_64_20230116/
 
 # create symlinks for all created binaries

install.py

@@ -142,6 +142,7 @@ def extract_resources(args):
         extract_all_zips_in_folder("data/dbSNP/inc_pseudogenes")
         extract_all_zips_in_folder("data/dbSNP/no_pseudogenes")
         extract_all_zips_in_folder("data/GRN")
+        extract_all_zips_in_folder("data/eqtl_mapping")
         extract_all_zips_in_folder("data/PositionBasedInputModule/snp_balanced_tree")
         extract_all_zips_in_folder("data/PositionBasedInputModule/snp_hashmaps")
         extract_all_zips_in_folder("data/PositionBasedInputModule/gene_balanced_tree")

test/e2e/test_container.sh

@@ -52,6 +52,22 @@ python ./run/NeEDL.py \
     "--ms-model" "PENETRANCE_NLL"
 
 
+# check that eqtl_mapping works
+python ./run/NeEDL.py \
+    --docker-image-name "$1" \
+    --docker-no-pulling \
+    "--num-threads" "1" \
+    "--output-directory" "$out_dir" \
+    "--input-format" "JSON_EPIGEN" \
+    "--input-path" "$dummy_dataset" \
+    "--phenotype" "DICHOTOMOUS" \
+    "--snp-annotate-eQTL" \
+    "--network-BIOGRID" \
+    "--ms-seeding-routine" "RANDOM_CONNECTED" \
+    "--ms-rc-start-seeds" "5" \
+    "--ms-model" "PENETRANCE_NLL"
+
+
 # test that custom annotation files and custom networks work
 annotation_file=$(realpath ./data/e2e_tests/annotations.csv)
 network_file=$(realpath ./data/e2e_tests/network.csv)