From 76c2b58b929cda1d684ddc0fce1b1b834669c97a Mon Sep 17 00:00:00 2001 From: Sara JC Gosline Date: Wed, 22 May 2024 09:37:50 -0700 Subject: [PATCH] updated HCMI to include more metadata --- build/hcmi/01-createHCMISamplesFile.py | 62 +- build/hcmi/02-getHCMIData.py | 6 +- build/hcmi/full_manifest.txt | 3402 +++++++++++++++--------- build/hcmi/hcmi_cancer_types.csv | 125 +- 4 files changed, 2252 insertions(+), 1343 deletions(-) mode change 100755 => 100644 build/hcmi/full_manifest.txt diff --git a/build/hcmi/01-createHCMISamplesFile.py b/build/hcmi/01-createHCMISamplesFile.py index 392be0f0..b0ad25e9 100755 --- a/build/hcmi/01-createHCMISamplesFile.py +++ b/build/hcmi/01-createHCMISamplesFile.py @@ -4,6 +4,10 @@ import argparse import numpy as np + + + + def align_to_linkml_schema(input_df): """ Maps the 'model_type' column of the input DataFrame to a set of predefined categories @@ -123,11 +127,18 @@ def fetch_metadata_for_samples(uuids): "fields": ( "cases.sample_ids," "cases.case_id," + "cases.submitter_id," + "cases.annotations.case_submitter_id," "cases.samples.sample_id," "cases.samples.portions.analytes.aliquots.aliquot_id," "cases.samples.sample_type," + "cases.diagnoses.submitter_id," + "cases.diagnoses.diagnosis_id," + "cases.diagnoses.classification_of_tumor," "cases.diagnoses.tissue_or_organ_of_origin," "cases.diagnoses.primary_diagnosis," + "cases.diagnoses.treatments.treatment_id,"##getting these but ignoring for now + "cases.diagnoses.treatments.submitter_id," ##getting these but ignoring for now "cases.samples.tumor_descriptor," "cases.samples.composition" ), @@ -158,23 +169,27 @@ def extract_data(data): for idx, sample in enumerate(case['samples']): for portion in sample['portions']: for analyte in portion['analytes']: + for aliquot in analyte['aliquots']: if idx < len(case['diagnoses']): diagnosis = case['diagnoses'][idx] extracted.append({ - 'id': hit['id'], - 'case_id': case['case_id'], + 'entry_id': hit['id'], + 'case_uuid': case['case_id'], + 'case_id': case['submitter_id'], 'tissue_or_organ_of_origin': diagnosis['tissue_or_organ_of_origin'], 'primary_diagnosis': diagnosis['primary_diagnosis'], + 'diagnosis_id':diagnosis['submitter_id'], + 'tumor_classification':diagnosis['classification_of_tumor'], 'sample_id': sample['sample_id'], 'sample_type': sample['sample_type'], - 'tumor_descriptor': sample.get('tumor_descriptor', None), + #'tumor_descriptor': sample.get('tumor_descriptor', None), 'composition': sample.get('composition', None), - 'aliquot_id': aliquot['aliquot_id'] + 'id': aliquot['aliquot_id'] }) return pd.DataFrame(extracted) -def filter_and_subset_data(df,sampfile): +def filter_and_subset_data(df,sampfile,mapfile): """ Filter and subset the data. @@ -182,7 +197,7 @@ def filter_and_subset_data(df,sampfile): Parameters ---------- - df : pandas dataframe + df : a tidied pandas dataframe full samples table Returns @@ -190,27 +205,37 @@ def filter_and_subset_data(df,sampfile): Pandas Dataframe """ duplicates_mask = df.drop('id', axis=1).duplicated(keep='first') + cmap = pd.read_csv(mapfile, encoding='ISO-8859-1') filt = df[~duplicates_mask] - filt= filt.drop_duplicates(subset='aliquot_id', keep=False) + filt= filt.drop_duplicates()#(subset='id', keep=False) + filt = pd.merge(filt,cmap,right_on=['tissue_or_organ_of_origin','primary_diagnosis'],left_on=['tissue_or_organ_of_origin','primary_diagnosis'],how='left') filt = filt.rename( - columns={"tissue_or_organ_of_origin":"common_name", - "primary_diagnosis": "cancer_type", - "composition": "model_type", - "case_id": "other_names", - "aliquot_id": "other_id"} + columns={"composition": "model_type", + "case_id": "common_name", + "id": "other_names"} + #"id": "sample_uuid"} ) - filt = filt[["cancer_type","common_name","other_names","other_id","model_type"]] - filt["other_id_source"] = "HCMI" + ##now we can melt all the identiers into other_id and other_id_source + longtab = pd.melt(filt, id_vars=['common_name','other_names','model_type','cancer_type'], value_vars=['diagnosis_id','tumor_classification','sample_type']) + longtab = longtab.rename(columns={'variable':'other_id_source','value':'other_id'}).drop_duplicates() + # filt = filt[["cancer_type","common_name","other_names","other_id","model_type"]] +# filt["other_id_source"] = "HCMI" # Create new improve sample IDs #Non-docker: # maxval = max(pd.read_csv('../cptac/cptac_samples.csv').improve_sample_id) # Docker: maxval = max(pd.read_csv(sampfile).improve_sample_id) - mapping = {other_id: i for i, other_id in enumerate(filt['other_id'].unique(), start=(int(maxval)+1))} + alluuids = list(set(longtab.other_names)) + + mapping = pd.DataFrame.from_dict( + {"other_names": [str(a) for a in alluuids], + "improve_sample_id": range(int(maxval)+1,int(maxval)+len(alluuids)+1) + }) + longtab = pd.merge(longtab,mapping,on='other_names',how='left') # Use the map method to create the new column based on the lab-id column - filt['improve_sample_id'] = filt['other_id'].map(mapping) - return filt + #['improve_sample_id'] = longtab['other_id'].map(mapping) + return longtab def main(): @@ -240,6 +265,7 @@ def main(): """ parser = argparse.ArgumentParser() parser.add_argument('--samples',dest='samps',help='Previous sample file') + parser.add_argument('--mapfile',dest='map',help='Mapping to common_cancer from primary_diagnosis and tissue_or_organ_of_origin',default='hcmi_cancer_types.csv') args = parser.parse_args() manifest_path = "full_manifest.txt" #manifest_url = "https://raw.githubusercontent.com/PNNL-CompBio/candleDataProcessing/hcmi_update/hcmi/full_manifest.txt" @@ -247,7 +273,7 @@ def main(): uuids = extract_uuids_from_manifest(manifest_path) metadata = fetch_metadata_for_samples(uuids) df = extract_data(metadata) - output = filter_and_subset_data(df,args.samps) + output = filter_and_subset_data(df,args.samps,args.map) aligned = align_to_linkml_schema(output) print(aligned) aligned.to_csv("/tmp/hcmi_samples.csv",index=False) diff --git a/build/hcmi/02-getHCMIData.py b/build/hcmi/02-getHCMIData.py index 399a0930..d875c6c2 100644 --- a/build/hcmi/02-getHCMIData.py +++ b/build/hcmi/02-getHCMIData.py @@ -430,7 +430,7 @@ def align_to_schema(data, data_type, chunksize=7500,samples_path='/tmp/hcmi_samp """ # samples_path = "/tmp/hcmi_samples.csv" samples = pl.read_csv(samples_path) - samples = samples.drop(["cancer_type", "common_name", "other_names", "model_type", "other_id_source"]) + samples = samples.drop(["cancer_type", "common_name", "other_id", "model_type", "species","other_id_source"]).unique() # Determine columns to select based on data_type columns = { @@ -448,8 +448,8 @@ def align_to_schema(data, data_type, chunksize=7500,samples_path='/tmp/hcmi_samp chunk = chunk.rename({"Variant_Classification": "variant_classification"}) chunk = chunk.select(selected_columns) - merged_chunk = samples.join(chunk, left_on='other_id', right_on='aliquot_id', how='inner') - merged_chunk = merged_chunk.drop(["aliquot_id", "other_id"]) + merged_chunk = samples.join(chunk, left_on='other_names', right_on='aliquot_id', how='inner') + merged_chunk = merged_chunk.drop(["aliquot_id", "other_names"]) # Append the processed chunk merged_data = pl.concat([merged_data, merged_chunk]) diff --git a/build/hcmi/full_manifest.txt b/build/hcmi/full_manifest.txt old mode 100755 new mode 100644 index 0258cc13..546b9db8 --- a/build/hcmi/full_manifest.txt +++ b/build/hcmi/full_manifest.txt @@ -1,1320 +1,2192 @@ id filename md5 size state -60a168ac-a1a9-4408-b3ef-4d8d8f0a0d4a 9a30e8b7-c976-4bd1-b342-9b76077f81fd.wgs.ASCAT.gene_level.copy_number_variation.tsv 917db52b334b8a2030a131fbe0083143 3442673 released -813c1c77-5032-4f91-92e1-7e840bd8f236 c4d72558-9c44-462c-8249-011bd2b0ea62.wgs.ASCAT.gene_level.copy_number_variation.tsv 39760a90307358f37bf93cae509823a8 3442781 released -40721c92-bdc1-4a2f-a355-1eb2a959fd2f 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+58ff0272-8975-4b7e-ad4e-2fe552c3a3f8 a62bdde0-3d57-4a01-a328-1e14e6906ce0.wxs.aliquot_ensemble_masked.maf.gz 11e4ddfd3a63c043da0f8447673d4e2f 17744 released diff --git a/build/hcmi/hcmi_cancer_types.csv b/build/hcmi/hcmi_cancer_types.csv index 29ad0030..3fdcff53 100755 --- a/build/hcmi/hcmi_cancer_types.csv +++ b/build/hcmi/hcmi_cancer_types.csv @@ -1,57 +1,68 @@ -cancer_type,common_name,new_cancer_type -Adenocarcinoma metastatic NOS,Ampulla of Vater, -Adenocarcinoma NOS,Ampulla of Vater, -Infiltrating duct carcinoma NOS,Ampulla of Vater, -Neuroendocrine carcinoma NOS,Ampulla of Vater, -Ewing sarcoma,Bone NOS, -Osteosarcoma NOS,Bone NOS, -Undifferentiated sarcoma,Bone NOS, -Not Reported,Bone NOS, -Glioblastoma,Brain NOS,Glioblastoma multiforme -Gliosarcoma,Brain NOS, -Metaplastic carcinoma NOS,Breast NOS,Breast carcinoma -Pleomorphic carcinoma,Breast NOS,Breast carcinoma -Carcinoma NOS,Breast NOS,Breast carcinoma -Infiltrating duct carcinoma NOS,Breast NOS,Breast carcinoma -Adenocarcinoma NOS,Colon NOS,Colon adenocarcinoma -Tubular adenoma NOS,Colon NOS, -Tubulovillous adenoma NOS,Colon NOS, -Adenocarcinoma intestinal type,Colon NOS,Colon adenocarcinoma -Adenocarcinoma metastatic NOS,Colon NOS,Colon adenocarcinoma -Medullary carcinoma NOS,Colon NOS, -Serrated adenoma,Colon NOS, -Mucinous adenocarcinoma,Colon NOS,Colon adenocarcinoma -Carcinoma NOS,Colon NOS, -Alveolar rhabdomyosarcoma,Connective subcutaneous and other soft tissues NOS,Sarcoma -Spindle cell sarcoma,Connective subcutaneous and other soft tissues NOS,Sarcoma -Epithelioid sarcoma,Connective subcutaneous and other soft tissues NOS,Sarcoma -Not Reported,Connective subcutaneous and other soft tissues NOS,Sarcoma -Adenocarcinoma NOS,Esophagus NOS, -Carcinoma NOS,Esophagus NOS, -Adenocarcinoma metastatic NOS,Esophagus NOS, -Adenocarcinoma NOS,Extrahepatic bile duct, -Noninfiltrating intraductal papillary adenocarcinoma,Gallbladder, -Cholangiocarcinoma,Intrahepatic bile duct, -Nephroblastoma NOS,Kidney NOS, -Adenocarcinoma NOS,Lung NOS,Lung adenocarcinoma -Carcinoma NOS,Lung NOS, -Mixed type rhabdomyosarcoma,Lung NOS, -Intraductal papillary-mucinous carcinoma invasive,Not Reported, -Serrated adenoma,Not Reported, -Mucinous adenocarcinoma,Ovary, -Infiltrating duct carcinoma NOS,Pancreas NOS, -Adenocarcinoma NOS,Pancreas NOS, -Mucinous adenocarcinoma,Pancreas NOS, -Adenocarcinoma metastatic NOS,Pancreas NOS, -Adenocarcinoma NOS,Rectosigmoid junction, -Adenocarcinoma NOS,Rectum NOS, -Mucinous adenocarcinoma,Rectum NOS, -Malignant melanoma NOS,Skin NOS,Melanoma -Not Reported,Skin NOS,Melanoma -Spindle cell sarcoma,Skin NOS, -Adenocarcinoma NOS,Small intestine NOS, -Tubulovillous adenoma NOS,Small intestine NOS, -Atypical carcinoid tumor,Small intestine NOS, -Adenocarcinoma NOS,Stomach NOS, -Carcinoma NOS,Stomach NOS, -Adenocarcinoma metastatic NOS,Stomach NOS, \ No newline at end of file +primary_diagnosis,tissue_or_organ_of_origin,cancer_type +"Adenocarcinoma metastatic, NOS",Ampulla of Vater,Ampulla of Vater cancer +"Adenocarcinoma, NOS",Ampulla of Vater,Ampulla of Vater cancer +"Infiltrating duct carcinoma, NOS",Ampulla of Vater,Ampulla of Vater cancer +"Neuroendocrine carcinoma, NOS",Ampulla of Vater,Ampulla of Vater cancer +Ewing sarcoma,"Bone, NOS",Ewing sarcoma +"Osteosarcoma, NOS","Bone, NOS",Osteosarcoma +Undifferentiated sarcoma,"Bone, NOS",Rare cancers +Not Reported,"Bone, NOS",Ewings sarcoma +Glioblastoma,"Brain, NOS",Glioblastoma +Gliosarcoma,"Brain, NOS",Glioblastoma +"Metaplastic carcinoma, NOS","Breast, NOS",Breast cancer +Pleomorphic carcinoma,"Breast, NOS",Breast cancer +"Carcinoma, NOS","Breast, NOS",Breast cancer +"Infiltrating duct carcinoma, NOS","Breast, NOS",Breast cancer +"Adenocarcinoma, NOS","Colon, NOS",Colon cancer +"Tubular adenoma, NOS","Colon, NOS",Colon cancer +"Tubulovillous adenoma, NOS","Colon, NOS",Colon cancer +Adenocarcinoma intestinal type,"Colon, NOS",Colon cancer +"Adenocarcinoma metastatic, NOS","Colon, NOS",Colon cancer +"Medullary carcinoma, NOS","Colon, NOS",Colon cancer +Serrated adenoma,"Colon, NOS",Colon cancer +Mucinous adenocarcinoma,"Colon, NOS",Colon cancer +"Carcinoma, NOS","Colon, NOS",Colon cancer +Alveolar rhabdomyosarcoma,"Connective subcutaneous and other soft tissues, NOS",Rhabdomyosarcoma +Spindle cell sarcoma,"Connective subcutaneous and other soft tissues, NOS",Rare cancers +Epithelioid sarcoma,"Connective subcutaneous and other soft tissues, NOS",Rare cancers +Not Reported,"Connective subcutaneous and other soft tissues, NOS",Sarcoma +"Adenocarcinoma, NOS","Esophagus, NOS",Esophageal cancer +"Carcinoma, NOS","Esophagus, NOS",Esophageal cancer +"Adenocarcinoma metastatic, NOS","Esophagus, NOS",Rare cancers +"Adenocarcinoma, NOS",Extrahepatic bile duct,Rare cancers +Noninfiltrating intraductal papillary adenocarcinoma,Gallbladder,Rare cancers +Cholangiocarcinoma,Intrahepatic bile duct,Intrahepatic bile duct cancer +"Nephroblastoma, NOS","Kidney, NOS",Wilms tumor +"Adenocarcinoma, NOS","Lung, NOS",Lung cancer +"Carcinoma, NOS","Lung, NOS",Lung cancer +Mixed type rhabdomyosarcoma,"Lung, NOS",Lung cancer +Intraductal papillary-mucinous carcinoma invasive,Not Reported,Other +Serrated adenoma,Not Reported,Other +Mucinous adenocarcinoma,Ovary,Ovarian cancer +"Infiltrating duct carcinoma, NOS","Pancreas, NOS",Pancreatic cancer +"Adenocarcinoma, NOS","Pancreas, NOS",Pancreatic cancer +Mucinous adenocarcinoma,"Pancreas, NOS",Pancreatic cancer +"Adenocarcinoma metastatic, NOS","Pancreas, NOS",Pancreatic cancer +"Adenocarcinoma, NOS",Rectosigmoid junction,Colon cancer +"Adenocarcinoma, NOS","Rectum, NOS",Colon cancer +Mucinous adenocarcinoma,"Rectum, NOS",Colon cancer +"Malignant melanoma, NOS","Skin, NOS",Melanoma +Not Reported,"Skin, NOS",Melanoma +Spindle cell sarcoma,"Skin, NOS",Melanoma +"Adenocarcinoma, NOS","Small intestine, NOS",Rare cancers +"Tubulovillous adenoma, NOS","Small intestine, NOS",Other +Atypical carcinoid tumor,"Small intestine, NOS",Rare cancers +"Adenocarcinoma, NOS","Stomach, NOS",Stomach cancer +"Carcinoma, NOS","Stomach, NOS",Stomach cancer +"Adenocarcinoma metastatic, NOS","Stomach, NOS",Stomach cancer +"Adenocarcinoma, intestinal type","Colon, NOS",Colon cancer +"Adenocarcinoma, metastatic, NOSĘ",Ampulla of Vater,Ampulla of Vater cancer +Alveolar rhabdomyosarcoma,"Connective, subcutaneous and other soft tissues",Rhabdomyosarcoma +Epithelioid sarcoma,"Connective, subcutaneous and other soft tissues",Rare cancers +"Intraductal papillary-mucinous carcinoma, invasive",Not Reported,Other +Spindle cell sarcoma,"Connective, subcutaneous and other soft tissues",Rare cancers +Not Reported,"Connective, subcutaneous and other soft tissues",Other +"Adenocarcinoma, metastatic, NOS","Colon, NOS",Colon cancer +"Adenocarcinoma, metastatic, NOS","Pancreas, NOS",Pancreatic cancer +"Adenocarcinoma, metastatic, NOS","Esophagus, NOS",Esophageal cancer +"Adenocarcinoma, metastatic, NOS","Stomach, NOS",Stomach cancer