checkQC.parsers.interop_parser module

class checkQC.parsers.interop_parser.InteropParser(runfolder, parser_configurations, *args, **kwargs)[source]

Bases: checkQC.parsers.parser.Parser

This Parser will get data from the Illumina Interop binary files, and send it to its subscribers as a tuple with the first element being the name of the element and the second one being a the actual data.

At this point the following data which is fetched from the Interop files and is sent in the following format:

  • (“error_rate”, {“lane”: <lane nbr>, “read”: <read nbr>, “error_rate”: <error rate>}))
  • (“percent_q30”, {“lane”: <lane nbr>, “read”: <read nbr>, “percent_q30”: <percent q30>}))
static get_non_index_reads(summary)[source]

Pick-out the reads which are not index reads

Parameters:summary – a Interop read summary object to parse the read numbers from
Returns:all reads which are not index reads

All Parsers must implement this method. Calling it should parse the data, what ever that means in the particular context, and send this data to its subscribers.

The run method should send data to the parsers subscribers using the _send_to_subscribers method.