saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO
https://saketkc.github.io/pysradb
BSD 3-Clause "New" or "Revised" License
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[BUG] library name not reported #84

Closed Phlya closed 3 years ago

Phlya commented 3 years ago

Describe the bug The entry library_name is not reported in the sra_metadata output.

To Reproduce

db.sra_metadata('SRX2792593', detailed=True).columns
Index(['run_accession', 'study_accession', 'experiment_accession',
       'experiment_title', 'experiment_desc', 'organism_taxid ',
       'organism_name', 'library_strategy', 'library_source',
       'library_selection', 'library_layout', 'sample_accession',
       'sample_title', 'instrument', 'total_spots', 'total_size',
       'run_total_spots', 'run_total_bases', 'run_alias', 'sra_url',
       'experiment_alias', 'isolate', 'age', 'biomaterial_provider', 'sex',
       'tissue', 'cell_line', 'treatment', 'BioSampleModel', 'ena_fastq_http',
       'ena_fastq_http_1', 'ena_fastq_http_2', 'ena_fastq_ftp',
       'ena_fastq_ftp_1', 'ena_fastq_ftp_2'],
      dtype='object')

While in the online view of this experiment it is available: https://www.ncbi.nlm.nih.gov/sra/SRX2792593

Desktop (please complete the following information):

saketkc commented 3 years ago

Closed by #85