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[GEN-1408] PoC: Remove rows of data containing SEQ_ASSAY_ID that are filtered out #573

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[GEN-1408] PoC: Remove rows of data containing SEQ_ASSAY_ID that are filtered out #573

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20 changes: 10 additions & 10 deletions genie/consortium_to_public.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,9 +63,6 @@ def consortiumToPublic(
database_to_staging.GENIE_RELEASE_DIR,
"data_cna_hg19.seg",
)
combined_bed_path = os.path.join(
database_to_staging.GENIE_RELEASE_DIR, "genie_combined.bed"
)

if not os.path.exists(database_to_staging.GENIE_RELEASE_DIR):
os.mkdir(database_to_staging.GENIE_RELEASE_DIR)
Expand Down Expand Up @@ -311,17 +308,20 @@ def consortiumToPublic(
version_comment=genie_version,
name="data_cna_hg19.seg",
)
elif entName == "genomic_information.txt":
bed = syn.get(entId, followLink=True)
bedDf = pd.read_csv(bed.path, sep="\t")
bedDf = bedDf[bedDf.SEQ_ASSAY_ID.isin(allClin.SEQ_ASSAY_ID)]
bedDf.to_csv(combined_bed_path, sep="\t", index=False)
elif entName in ["genomic_information.txt", "assay_information.txt"]:
file_with_seq_assay_ent = syn.get(entId, followLink=True)
file_with_seq_assay_df = pd.read_csv(file_with_seq_assay_ent.path, sep="\t")
file_with_seq_assay_df = file_with_seq_assay_df[file_with_seq_assay_df.SEQ_ASSAY_ID.isin(allClin.SEQ_ASSAY_ID)]
file_path = os.path.join(
database_to_staging.GENIE_RELEASE_DIR, entName
)
file_with_seq_assay_df.to_csv(file_path, sep="\t", index=False)
load.store_file(
syn=syn,
filepath=combined_bed_path,
filepath=file_path,
parentid=public_release_preview,
version_comment=genie_version,
name="genomic_information.txt",
name=entName,
)
else:
ent = syn.get(entId, followLink=True, downloadFile=False)
Expand Down
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