frontier.IO package

Submodules

frontier.IO.AQCReader module

frontier.IO.AbstractReader module

class frontier.IO.AbstractReader.AbstractReader(filepath, CLASSES, auto_close, header)

Bases: object

Wraps a file handler and provides controlled access to its contents.

close()

Close the file handler.

get_data()

Return read data.

get_id()

Return record ID.

process_file()

Calls process_line for each line in input file.

process_line(line)

Process a record of the input file.

frontier.IO.BamcheckReader module

class frontier.IO.BamcheckReader.BamcheckReader(filepath, CLASSES=None, auto_close=True)

Bases: frontier.IO.AbstractReader.AbstractReader

Wraps a file handler and provides access to bamcheckr’d file contents.

get_data()

Return read summary data.

get_id()

process_line(line)

Process a record of the bamcheckr’d file.

class frontier.IO.BamcheckReader.IndelDistribution

Bases: object

Novel object to hold a trio of lengths, inserts and deletes counters.

total_deletes()

Return sum of total deletes.

total_inserts()

Return sum of total inserts.

class frontier.IO.BamcheckReader.SummaryNumbers(*args)

Bases: dict

Wraps a dictionary and provides functionality to search for keys.

search(query)

Search the structure for keys matching a given query.

frontier.IO.BamcheckReader.tidy_key(key)

Sanitize summary number key.

frontier.IO.NotImplementedReader module

Module contents