acore.io package

download_PRIDE_data(pxd_id, file_name, to='.', user='', password='', date_field='publicationDate') → dict

This function downloads a project file from the PRIDE repository. To see more of the pride API, have a look at https://www.ebi.ac.uk/pride/ws/archive/v3/webjars/swagger-ui/index.html or EBI’s commandline tool pridepy PRIDE-Archive/pridepy

Parameters:

• pxd_id (str) – PRIDE project identifier (id. PXD013599).

• file_name (str) – name of the file to dowload

• to (str) – local directory where the file should be downloaded

• user (str) – username to access biomedical database server if required.

• password (str) – password to access biomedical database server if required.

• date_field (str) – projects deposited in PRIDE are search based on date, either submissionData or publicationDate (default)

unrar(filepath, to)

Decompress RAR file :param str filepath: path to rar file :param str to: where to extract all files

download_file(url: str, local_filename: str) → None

Download a file from the internet.

Subpackages

• acore.io.uniprot package
  • fetch_annotations()
  • process_annotations()
  • Submodules
    • acore.io.uniprot.uniprot module
      • check_response()
      • submit_id_mapping()
      • get_next_link()
      • check_id_mapping_results_ready()
      • get_batch()
      • combine_batches()
      • get_id_mapping_results_link()
      • decode_results()
      • get_xml_namespace()
      • merge_xml_results()
      • print_progress_batches()
      • get_id_mapping_results_search()
      • get_id_mapping_results_stream()

Submodules

• acore.io.download module
  • download_file()
• acore.io.ftp module
  • download_from_ftp()
• acore.io.kegg module
  • link_kegg_batch()
  • fetch_kegg_ko_descriptions()
  • cid_to_kegg_id()
  • parse_compound_pathway_mapping()
  • parse_kegg_name_description()
  • lookup_cid_to_kegg_id()
• acore.io.pride module
  • download_PRIDE_data()
• acore.io.uncompress module
  • unrar()