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[DPE-1448] Adjust MAF validation #1

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Merged
rxu17 merged 4 commits into from
Oct 1, 2025
Merged

[DPE-1448] Adjust MAF validation #1

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3817213
remove unused code and refactor maf validation
rxu17 Sep 29, 2025
1fb194f
correct readme, add python restriction
rxu17 Oct 1, 2025
59cea84
Merge branch 'main' into dpe-1448-adjust-maf-validation
rxu17 Oct 1, 2025
06dea06
correct pyyaml version
rxu17 Oct 1, 2025
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -221,7 +221,7 @@ python3 clinical.py
--cli_to_oncotree_mapping_synid syn66313842 \
--datahub_tools_path /<some_path>/datahub-study-curation-tools \
--lens_id_mapping_synid syn68826836
--neoantigen-data-synid syn21841882
--neoantigen_data_synid syn21841882
```

Run maf processing
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2 changes: 2 additions & 0 deletions pyproject.toml
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Expand Up @@ -2,9 +2,11 @@
[project]
name = "cbioportal_export"
version = "0.1.0"
requires-python = ">=3.9,<3.12"
dependencies = [
"synapseclient[pandas]>=4,<5",
"pandas>=2.2",
"pyyaml=6.0"
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Copilot AI Oct 1, 2025

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The dependency specification uses '=' instead of the correct '==' operator for version pinning. This should be 'pyyaml==6.0' to properly specify the exact version.

Suggested change
"pyyaml=6.0"
"pyyaml==6.0"

Copilot uses AI. Check for mistakes.
]

[dependency-groups]
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25 changes: 3 additions & 22 deletions src/iatlascbioportalexport/load.py
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Expand Up @@ -4,7 +4,6 @@
import sys

import synapseclient
import synapseutils

import utils

Expand Down Expand Up @@ -49,44 +48,26 @@ def save_to_synapse(
dataset_name (str): name of the iatlas dataset to save to
synapse
datahub_tools_path (str): Path to the datahub tools repo
output_folder_synid (str): Synapse id of the output folder
output_folder_synid (str): Synapse id of the outputs folder
version_comment (str): Version comment for this iteration of files on synapse. Optional.
Defaults to None.
"""
# TODO: Make into argument
dataset_dir = os.path.join(datahub_tools_path, "add-clinical-header", dataset_name)
# see if dataset_folder exists
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@rxu17 rxu17 Sep 30, 2025

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Remove code as we just need to input the output folder synapse id directly instead of trying to create one inside the project

dataset_folder_exists = False
for _, directory_names, _ in synapseutils.walk(syn=syn, synId=output_folder_synid):
directories = directory_names # top level directories
break

for dataset_folder in directories:
if dataset_name == dataset_folder[0]:
dataset_folder_exists = True
dataset_folder_id = dataset_folder[1]
break

if not dataset_folder_exists:
new_dataset_folder = synapseclient.Folder(
dataset_name, parent=output_folder_synid
)
dataset_folder_id = syn.store(new_dataset_folder).id

# store required files
for file in utils.REQUIRED_OUTPUT_FILES:
syn.store(
synapseclient.File(
f"{dataset_dir}/{file}",
name=file,
parent=dataset_folder_id,
parent=output_folder_synid,
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@danlu1 danlu1 Oct 1, 2025

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Do you want to save all files in the same level of repo?

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@rxu17 rxu17 Oct 1, 2025

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Yes, that is the expected folder structure. Case list files get their own folder within the output folder

version_comment=version_comment
)
)

# store case lists
case_list_files = os.listdir(os.path.join(dataset_dir, "case_lists"))
case_list_folder = synapseclient.Folder("case_lists", parent=dataset_folder_id)
case_list_folder = synapseclient.Folder("case_lists", parent=output_folder_synid)
try:
case_list_folder_id = syn.store(case_list_folder).id
except:
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139 changes: 1 addition & 138 deletions src/iatlascbioportalexport/maf.py
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Expand Up @@ -6,130 +6,10 @@
from typing import Dict

import pandas as pd
import synapseclient

import utils

my_agent = "iatlas-cbioportal/0.0.0"
syn = synapseclient.Synapse(user_agent=my_agent).login()

REQUIRED_MAF_COLS = [
"Hugo_Symbol",
"Entrez_Gene_Id",
"Center",
"NCBI_Build",
"Chromosome",
"Start_Position",
"End_Position",
"Strand",
"Consequence",
"Variant_Classification",
"Variant_Type",
"Reference_Allele",
"Tumor_Seq_Allele1",
"Tumor_Seq_Allele2",
"dbSNP_RS",
"dbSNP_Val_Status",
"Tumor_Sample_Barcode",
"Matched_Norm_Sample_Barcode",
"Match_Norm_Seq_Allele1",
"Match_Norm_Seq_Allele2",
"Tumor_Validation_Allele1",
"Tumor_Validation_Allele2",
"Match_Norm_Validation_Allele1",
"Match_Norm_Validation_Allele2",
"Verification_Status",
"Validation_Status",
"Mutation_Status",
"Sequencing_Phase",
"Sequence_Source",
"Validation_Method",
"Score",
"BAM_File",
"Sequencer",
"n_ref_count",
"n_alt_count",
"HGVSc",
"HGVSp",
"HGVSp_Short",
"Transcript_ID",
"RefSeq",
"Protein_position",
"Codons",
"Exon_Number",
"AA_AF",
"AF",
"AFR_AF",
"ALLELE_NUM",
"AMR_AF",
"ASN_AF",
"Allele",
"Amino_acids",
"BIOTYPE",
"CANONICAL",
"CCDS",
"CDS_position",
"CLIN_SIG",
"DISTANCE",
"DOMAINS",
"EAS_AF",
"EA_AF",
"ENSP",
"EUR_AF",
"EXON",
"Existing_variation",
"FILTER",
"Feature",
"Feature_type",
"GENE_PHENO",
"Gene",
"HGNC_ID",
"HGVS_OFFSET",
"HIGH_INF_POS",
"IMPACT",
"INTRON",
"MINIMISED",
"MOTIF_NAME",
"MOTIF_POS",
"MOTIF_SCORE_CHANGE",
"PHENO",
"PICK",
"PUBMED",
"PolyPhen",
"SAS_AF",
"SIFT",
"SOMATIC",
"STRAND_VEP",
"SWISSPROT",
"SYMBOL",
"SYMBOL_SOURCE",
"TREMBL",
"TSL",
"UNIPARC",
"VARIANT_CLASS",
"all_effects",
"cDNA_position",
"flanking_bps",
"genomic_location_explanation",
"gnomADe_AF",
"gnomADe_AFR_AF",
"gnomADe_AMR_AF",
"gnomADe_ASJ_AF",
"gnomADe_EAS_AF",
"gnomADe_FIN_AF",
"gnomADe_NFE_AF",
"gnomADe_OTH_AF",
"gnomADe_SAS_AF",
"n_depth",
"t_depth",
"t_ref_count",
"t_alt_count",
"vcf_id",
"vcf_pos",
"vcf_qual",
"Annotation_Status",
]

syn = utils.synapse_login()

def read_and_merge_maf_files(input_folder_synid: str) -> pd.DataFrame:
"""Read in and merge MAF files from a specified folder
Expand Down Expand Up @@ -383,20 +263,6 @@ def validate_that_allele_freq_are_not_na(
)


def validate_that_required_columns_are_present(
input_df: pd.DataFrame, **kwargs
) -> None:
"""Validate that required set of maf columns are present

Args:
input_df (pd.DataFrame): _description_
"""
logger = kwargs.get("logger", logging.getLogger(__name__))
if set(REQUIRED_MAF_COLS) != set(list(input_df.columns)):
missing_cols = set(REQUIRED_MAF_COLS) - set(list(input_df.columns))
logger.error(f"Missing required columns in maf: {list(missing_cols)}")


def main():
parser = argparse.ArgumentParser()
parser.add_argument(
Expand Down Expand Up @@ -464,9 +330,6 @@ def main():
validate_export_files(
input_df=maf_df, output_df=mafs["annotated_maf"], logger=dataset_logger
)
validate_that_required_columns_are_present(
mafs["annotated_maf"], logger=dataset_logger
)
validate_that_allele_freq_are_not_na(mafs["annotated_maf"], logger=dataset_logger)
generate_meta_files(
dataset_name=args.dataset, datahub_tools_path=args.datahub_tools_path
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1 change: 0 additions & 1 deletion src/iatlascbioportalexport/utils.py
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Expand Up @@ -19,7 +19,6 @@
"meta_gene_signatures.txt",
"data_rna_seq_mrna.txt",
"meta_rna_seq_mrna.txt",
"cbioportal_validator_output.txt",
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@danlu1 danlu1 Oct 1, 2025

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Did you track why this file is removed?

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@rxu17 rxu17 Oct 1, 2025

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I think my comment got lost in the old orca-recipes repo but this is removed as it's not a required file we need to run validation on haha

]


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