sra_metadata_processing module

sra_metadata_processing.parse_all_fields_csv(files, outpath)[source]

Reads all csv files and produces one table with all fields

Parameters

  • files – as list

  • outpath – to table .csv

sra_metadata_processing.parse_xml(xml_files, csv_files)[source]

Reads xml files which are not consistent

Parameters

  • xml_files – as list

  • csv_files – as list

Returns

metadata: dict

sra_metadata_processing.write_xml_table(outpath, metadata)[source]

Write table with csv and xml info to table

Parameters

  • outpath – path to output table .csv

  • metadata – dict