Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[GEN-1026] Output annotation error report #544

Merged
merged 6 commits into from
Jan 11, 2024
Merged

[GEN-1026] Output annotation error report #544

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions Dockerfile
View file
Open in desktop
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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@rxu17 I'd comment this out for now and just rely on the latest version until we are actually able to pull this from a config file.

)

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
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Loading