vardb package

The vardb package contains utilities for loading and querying data in vardb. The contents of this package are used in other scripts and apis to build complex functionality.

Subpackages

• vardb.connections package
  • Submodules
  • vardb.connections.bioapps module
  • vardb.connections.bioapps_api module
  • vardb.connections.bioapps_sql module
  • vardb.connections.connection module
  • vardb.connections.karen module
  • vardb.connections.lims module
  • vardb.connections.vardb_connection module
  • vardb.connections.vardb_hdfs module
  • vardb.connections.vardb_loader module
• vardb.metadata_wrangling package
  • Subpackages
    • vardb.metadata_wrangling.oasis package
      • Submodules
      • vardb.metadata_wrangling.oasis.demographics module
      • vardb.metadata_wrangling.oasis.diagnosis module
      • vardb.metadata_wrangling.oasis.drug_map module
      • vardb.metadata_wrangling.oasis.error_code module
      • vardb.metadata_wrangling.oasis.helpers module
      • vardb.metadata_wrangling.oasis.oasis module
      • vardb.metadata_wrangling.oasis.output module
      • vardb.metadata_wrangling.oasis.preprocess module
      • vardb.metadata_wrangling.oasis.radiation module
      • vardb.metadata_wrangling.oasis.treatment module
  • Submodules
  • vardb.metadata_wrangling.configuration module
  • vardb.metadata_wrangling.get_bam_cnvs module
  • vardb.metadata_wrangling.helpers module
  • vardb.metadata_wrangling.loader_maker module
  • vardb.metadata_wrangling.locate_metadata_changes module
  • vardb.metadata_wrangling.metadata_collector module
• vardb.queries package
  • Submodules
  • vardb.queries.CNV_overlap module
  • vardb.queries.experimental_records module
  • vardb.queries.experimental_records_external module
• vardb.variant_data_files package
  • Submodules
  • vardb.variant_data_files.cnv module
  • vardb.variant_data_files.data_classes module
  • vardb.variant_data_files.expression module
  • vardb.variant_data_files.maf module
  • vardb.variant_data_files.variant_data_file module
  • vardb.variant_data_files.vcf module
  • vardb.variant_data_files.vcf_tools module
• vardb.variant_file_loaders package
  • Submodules
  • vardb.variant_file_loaders.loader module
  • vardb.variant_file_loaders.sample_metadata module

Submodules

vardb.tools module

Some helper functions. Currently the only one that is frequently used is the initialize_logger function.

class vardb.tools.StreamToLogger(logger, log_level=20)

Bases: object

Fake file-like stream object that redirects writes to a logger instance.

write(buf)

vardb.tools.get_login_from_file(filename)

Gets account info from ~/filename (.ginaccount for bioapps, .pgpass for vardb, .limsaccount for lims)

Returns:a string with username:password

vardb.tools.get_md5sum(path)

Gets md5sum for file

Returns:md5sum for the file

vardb.tools.initialize_logger(filename=None, logLevel='info', logLevel_streaming='warning')

Initializes a logger with the indicated filename. Also, sends stderr to the logger as well.

Parameters:filename –

vardb.tools.line_count(filename)

Just calculates the line count of a file

Parameters:filename – Returns:line count of file with filename

vardb.tools.production_error_handling(log_name)

This outer function handles passing the log name to the decorator.

Parameters:log_name – Name of the logger to use.