GTEx#

class openomics.database.annotation.GTEx(path='https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/', file_resources=None, col_rename=None, blocksize=0, verbose=False)[source][source]#

Bases: openomics.database.base.Database

Loads the database from https://www.gtexportal.org/home/ .

Default path: “https://storage.googleapis.com/gtex_analysis_v8/rna_seq_data/” . Default file_resources: {

“GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct”: “GTEx_Analysis_2017-06-05_v8_RNASeQCv1.1.9_gene_median_tpm.gct.gz”, “GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt”: “https://storage.googleapis.com/gtex_analysis_v8/annotations/GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt”, “GTEx_Analysis_2017-06-05_v8_RSEMv1.3.0_transcript_tpm.gct”: “GTEx_Analysis_2017-06-05_v8_RSEMv1.3.0_transcript_tpm.gct.gz”,

}

Attributes Summary

Methods Summary

load_dataframe(file_resources[, blocksize])

param file_resources

Attributes Documentation

COLUMNS_RENAME_DICT = {'Description': 'gene_name', 'Name': 'gene_id'}[source]#

Methods Documentation

load_dataframe(file_resources, blocksize=None)[source][source]#
Parameters
  • file_resources

  • blocksize

Return type

DataFrame