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

Jump to bottom

Update small_variants.py #21

Merged
merged 3 commits into from
Jun 3, 2024
Merged

Update small_variants.py #21

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
9e403bb
Update small_variants.py
May 31, 2024
698a720
adding option to override tumor barcode
May 31, 2024
475b436
remove extra argument
buehlere May 31, 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
37 changes: 30 additions & 7 deletions genotype_variants/commands/small_variants.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -397,7 +397,7 @@ def generate_gbcms_cmd(
)
@click_log.simple_verbosity_option(logger)
def merge(
patient_id, input_maf, input_standard_maf, input_duplex_maf, input_simplex_maf, sample_id
patient_id, input_maf, input_standard_maf, input_duplex_maf, input_simplex_maf, sample_id, tumor_name_override
):
"""
Given original input MAF used as an input for GBCMS along with
Expand Down Expand Up @@ -489,13 +489,15 @@ def merge(
)
exit(1)
if patient_id:
logger.info("small_variants: Patient ID: %s", patient_id)
outfile = patient_id
bam_id = patient_id
if sample_id:
logger.info("small_variants: Sample ID: %s", sample_id)
outfile = sample_id
bam_id = sample_id
logger.info("small_variants: ID: %s", bam_id)
outfile = bam_id
if d_maf is not None and s_maf is not None:
ds_maf = cdsd(s_maf, d_maf)
if tumor_name_override:
ds_maf['Tumor_Sample_Barcode'] = bam_id
file_name = pathlib.Path.cwd().joinpath(
outfile + "-SIMPLEX-DUPLEX" + "_genotyped.maf"
)
Expand All @@ -506,24 +508,32 @@ def merge(
(df_o_s_ds, df_o_s, df_s_ds, df_s_ds) = None, None, None, None
if o_maf is not None and i_maf is not None and ds_maf is not None:
df_o_s_ds = camd(o_maf, i_maf, ds_maf)
if tumor_name_override:
df_o_s_ds['Tumor_Sample_Barcode'] = bam_id
file_name = pathlib.Path.cwd().joinpath(
outfile + "-ORG-STD-SIMPLEX-DUPLEX" + "_genotyped.maf"
)
write_csv(file_name, df_o_s_ds)
elif o_maf is not None and i_maf is not None:
df_o_s = camd(o_maf, i_maf, None)
if tumor_name_override:
df_o_s['Tumor_Sample_Barcode'] = bam_id
file_name = pathlib.Path.cwd().joinpath(
outfile + "-ORG-STD" + "_genotyped.maf"
)
write_csv(file_name, df_o_s)
elif o_maf is not None and ds_maf is not None:
df_o_ds = camd(o_maf, None, ds_maf)
if tumor_name_override:
df_o_ds['Tumor_Sample_Barcode'] = bam_id
file_name = pathlib.Path.cwd().joinpath(
outfile + "-ORG-SIMPLEX-DUPLEX" + "_genotyped.maf"
)
write_csv(file_name, df_o_ds)
elif i_maf is not None and ds_maf is not None:
df_s_ds = camd(None, i_maf, ds_maf)
if tumor_name_override:
df_s_ds['Tumor_Sample_Barcode'] = bam_id
file_name = pathlib.Path.cwd().joinpath(
outfile + "-STD-SIMPLEX-DUPLEX" + "_genotyped.maf"
)
Expand All @@ -540,6 +550,8 @@ def merge(
file_name = pathlib.Path.cwd().joinpath(
outfile + "-SIMPLEX-DUPLEX" + "_genotyped.maf"
)
if tumor_name_override:
ds_maf['Tumor_Sample_Barcode'] = bam_id
write_csv(file_name, ds_maf)
t1_stop = time.perf_counter()
t2_stop = time.process_time()
Expand Down Expand Up @@ -709,6 +721,14 @@ def write_csv(file_name, data_frame):
type=click.STRING,
help="Override default sample name",
)
@click.option(
"-to",
"--tumor_name_override",
required=False,
is_flag=True,
default=False,
help="Override the MAF Tumor_Sample_Barcode name with the BAM Tumor Sample Barcode",
)
@click_log.simple_verbosity_option(logger)
def all(
input_maf,
Expand All @@ -722,7 +742,9 @@ def all(
fragment_count,
mapping_quality,
threads,
sample_id
sample_id,
tumor_name_override

):
"""
Command that helps to generate genotyped MAF and
Expand Down Expand Up @@ -766,8 +788,9 @@ def all(
sample_id
)
final_file = merge.callback(
patient_id, input_maf, standard_maf, duplex_maf, simplex_maf, sample_id
patient_id, input_maf, standard_maf, duplex_maf, simplex_maf, sample_id, tumor_name_override
)

t1_stop = time.perf_counter()
t2_stop = time.process_time()
logger.info("--------------------------------------------------")
Expand Down
2 changes: 1 addition & 1 deletion requirements_dev.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,6 @@ Sphinx==2.3.1
twine==3.1.1
Click==7.0
click-log==0.3.2
pandas==2.0.0
pandas
xlrd==1.2.0
numpy>=1.20.3
Loading