nucleus.io.converter -- A universal converter program for nucleus-supported genomics file formats.

Source code: nucleus/io/converter.py

Documentation index: doc_index.md

Invoked with a single argument, this program will open a genomics data file and iterate over its contents, doing no writing. This is a good benchmark for I/O and reader processing speed.

Invoked with two arguments, the program will open the first file, read its records, and write them, one at a time, to the second file. The filetypes for the first and second filename must be compatible ways of encoding the same nucleus genomics record type (for example, infile.gff and outfile.gff.tfrecord.gz are compatible, but infile.gff and outfile.bam are not.

Note: at present we have no convention for encoding a file header in tfrecords, so conversion is not possible from tfrecord to any native file format for which a header is compulsory.

Classes overview

Name Description
ConversionError An exception used to signal file conversion error.
NullWriter A writer class whose .write() method is a no-op.

Functions overview

Name Description
convert(in_filename, out_filename) Converts a recognized genomics file in_filename to out_filename.
main(argv)

Classes

ConversionError

An exception used to signal file conversion error.

NullWriter

A writer class whose .write() method is a no-op.

This allows us to create and use a writer object where one is required by
context but we do not wish to write to any file.

Methods:

__init__(self, unused_filename, header=None)

write(self, unused_record)

Functions

convert(in_filename, out_filename)

Converts a recognized genomics file `in_filename` to `out_filename`.

Args:
  in_filename: str; filename of a genomics data file to use as input.
  out_filename: str; filename of a genomics data file to use as output, or
    None, if no output should be written.

Raises:
  ConversionError, if the conversion could not be executed.

main(argv)