Skip to content

Fix sample_reconstruction_plots option for non-SBS96 signatures #197

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

Open
takahiro-blab wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Fix sample_reconstruction_plots option for non-SBS96 signatures #197

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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 SigProfilerAssignment/decomposition.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -92,6 +92,7 @@ def convert_PDF_to_PNG(input_file_name, output_directory, page_names):
def generate_sample_reconstruction(
cosmic_sigs,
samples_input,
mtype,
activities,
output_dir,
recon_output_types,
Expand All @@ -102,7 +103,6 @@ def generate_sample_reconstruction(
# both = pdf generation + png conversion
# png = pdf generation + png conversion + pdf removal
project = "test_run"
mtype = "96"

final_pdf = PdfWriter()
samples = samples_input.copy(deep=True)
Expand Down Expand Up @@ -1137,7 +1137,6 @@ def spa_analyze(
if (
isinstance(sample_reconstruction_plots, str)
and sample_reconstruction_plots.lower() in recon_output_types
and mutation_type == "96"
and signature_database is None
):
ss_recon_odir = os.path.join(
Expand All @@ -1153,6 +1152,7 @@ def spa_analyze(
generate_sample_reconstruction(
cosmic_sig_ref,
genomes,
mutation_type,
cosmic_activities,
ss_recon_odir,
sample_reconstruction_plots,
Expand Down