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[GEN-1026] Output annotation error report #544

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merged 6 commits into from
Jan 11, 2024
Merged

[GEN-1026] Output annotation error report #544

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cc081a1
update java version to match gn annotator.jar file, change tag versio…
rxu17 Jan 5, 2024
00f527e
use newer version of annotator.jar
rxu17 Jan 8, 2024
5c955cd
define error report dir
rxu17 Jan 8, 2024
d7b3bd0
add error dir changes to tests
rxu17 Jan 8, 2024
2267c4a
lint
rxu17 Jan 8, 2024
b3d6491
comment out version until we can pull from config file
rxu17 Jan 11, 2024
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4 changes: 2 additions & 2 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ RUN apt-get update && apt-get install -y --allow-unauthenticated --no-install-re
# texlive-generic-recommended \
texlive-latex-extra \
# genome nexus
openjdk-8-jre \
openjdk-11-jre \
# This is for reticulate
python3.8-venv && \
apt-get clean && \
Expand Down Expand Up @@ -83,6 +83,6 @@ WORKDIR /root/
# Must move this git clone to after the install of Genie,
# because must update cbioportal
RUN git clone https://github.com/cBioPortal/cbioportal.git -b v5.3.19
RUN git clone https://github.com/Sage-Bionetworks/annotation-tools.git -b 0.0.3
RUN git clone https://github.com/Sage-Bionetworks/annotation-tools.git -b 0.0.4

WORKDIR /root/Genie
4 changes: 4 additions & 0 deletions genie/process_mutation.py
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Expand Up @@ -202,12 +202,14 @@ def process_mutation_workflow(
"syn22053204",
ifcollision="overwrite.local",
downloadLocation=genie_config["genie_annotation_pkg"],
# version=1, # TODO: This should pull from a config file in the future
)
# Genome Nexus Jar file
syn.get(
"syn22084320",
ifcollision="overwrite.local",
downloadLocation=genie_config["genie_annotation_pkg"],
# version=13, # TODO: This should pull from a config file in the future
)

annotated_maf_path = annotate_mutation(
Expand Down Expand Up @@ -248,6 +250,7 @@ def annotate_mutation(
"""
input_files_dir = tempfile.mkdtemp(dir=workdir)
output_files_dir = tempfile.mkdtemp(dir=workdir)
error_dir = os.path.join(output_files_dir, f"{center}_error_reports")

for mutation_file in mutation_files:
move_mutation(mutation_file, input_files_dir)
Expand All @@ -260,6 +263,7 @@ def annotate_mutation(
os.path.join(genie_annotation_pkg, "annotation_suite_wrapper.sh"),
f"-i={input_files_dir}",
f"-o={output_files_dir}",
f"-e={error_dir}",
f"-m={merged_maf_path}",
f"-c={center}",
"-s=WXS",
Expand Down
4 changes: 4 additions & 0 deletions tests/test_process_mutation.py
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Expand Up @@ -104,11 +104,13 @@ def test_process_mutation_workflow(syn, genie_config):
"syn22053204",
ifcollision="overwrite.local",
downloadLocation=genie_annotation_pkg,
# version=1, # TODO: This should pull from a config file in the future
),
call(
"syn22084320",
ifcollision="overwrite.local",
downloadLocation=genie_annotation_pkg,
# version=13, # TODO: This should pull from a config file in the future
),
]
center = "SAGE"
Expand Down Expand Up @@ -148,6 +150,7 @@ def test_annotate_mutation():
workdir = "working/dir/path"
mktemp_calls = [call(dir=workdir)] * 2
input_dir = "input/dir"
error_dir = "input/dir/SAGE_error_reports"
with patch.object(
tempfile, "mkdtemp", return_value=input_dir
) as patch_mktemp, patch.object(
Expand All @@ -169,6 +172,7 @@ def test_annotate_mutation():
"annotation/pkg/path/annotation_suite_wrapper.sh",
f"-i={input_dir}",
f"-o={input_dir}",
f"-e={error_dir}",
f"-m=input/dir/data_mutations_extended_{center}.txt",
f"-c={center}",
"-s=WXS",
Expand Down
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