dinopy.shaping module

This module contains functions to shape q-grams.

Note

The dinopy.processors.qgrams() function that creates (shaped) q-grams from a sequence is considered a processor and can be found in the dinopy.processors module.

dinopy.shaping.apply_shape(qgram, shp)

Applies the given shape to the given q-gram. Calls _apply_shape_array() or _apply_shape_unicode(), depending on the type of q-gram.

Parameters:
Returns:

A reduced q-gram. The result of applying qgram_shape to qgram, e.g. applying #__## to ACGTA results in ATA.

Return type:

dtype

dinopy.shaping.windows(seq, qgram_shape)

Create all windows described by the shape from the seq.

Check the type of the input and invoke the right _windows_<type>

Parameters:

  • seq (dtype) – A sequence of any dtype.

  • qgram_shape – see dinopy.shape

Yields:

dtype – An iterator over all gapped q-grams generated by applying qgram_shape to all q-grams of seq.

Raises:

TypeError – If seq is of an unsupported type. Supported types are: - bytes - bytearray - string / unicode - array

dinopy.shaping.windows_list(seq, qgram_shape) → list

Check the type of the input and invoke the right _windows_<type> function to create all windows created by the given q-gram shape

Parameters:

  • seq (dtype) – A sequence of any dtype.

  • qgram_shape – see dinopy.shape

Returns:

A list containing all gapped q-grams generated by applying qgram_shape() to all q-grams of seq.

Return type:

list

Raises:

InvalidDtypeError – If the seq has an invalid dtype.