thoraxe.utils package

Submodules

thoraxe.utils.folders module

folders: Util functions to create output folder structure.

thoraxe.utils.folders.create_subfolder(folder, subfolder)

Return path to the subfolder. It creates the folder if it doesn’t exist.

thoraxe.utils.species module

species: Util functions to get the species list.

thoraxe.utils.species.check_species_name(species_name)

Return True if the species_name has the correct format.

The expected name is binomial. Trinomial names aren’t used but they don’t raise an error. If the species_name doesn’t conform the expected format an error is raised.

>>> check_species_name('homo_sapiens')
True
>>> check_species_name('colobus_angolensis_palliatus')
False
>>> check_species_name('cricetulus_griseus_chok1gshd')
False

thoraxe.utils.species.get_species_list(specieslist)

Return a list of species names (str).

>>> get_species_list('')
>>> get_species_list('homo_sapiens,mus_musculus')
['homo_sapiens', 'mus_musculus']

thoraxe.utils.split module

split: Util functions to split s-exons.

thoraxe.utils.split.split_exons(exons)

Return a list of the s-exons in the string.

>>> split_exons('3_0/3_1')
['3_0', '3_1']
>>> split_exons('4_0')
['4_0']

thoraxe.utils.split.split_lengths(lengths, seq)

Return a list of the s-exon lengths, len(seq) if there is not data.

>>> import numpy as np
>>> split_lengths('4/2', 'MLGHAC')
[4, 2]
>>> split_lengths('6', 'MLGHAC')
[6]
>>> split_lengths('', 'MLGHAC')
[6]
>>> split_lengths(np.nan, 'MLGHAC')
[6]

thoraxe.utils.split.split_seqs(sequences, seq)

Return a list with the s-exon sequences.

>>> split_seqs('MLGH/AC', 'MLGHAC')
['MLGH', 'AC']
>>> split_seqs('MLGHAC', 'MLGHAC')
['MLGHAC']
>>> split_seqs('', 'MLGHAC')
['MLGHAC']

thoraxe.utils.windows module

Windows: Functions useful for testing and Windows support.

thoraxe.utils.windows.is_windows()

Return True in Windows.

Module contents

utils: A collection of functions to use in different places of thoraxe.