<reponame>hclimente/spada<gh_stars>1-10
from spada.io import io
from spada.methods import summary

import os
import pytest

scriptPath = os.path.realpath(__file__)
dataPath = os.path.dirname(scriptPath) + "/../../data/"

def test_init():

	s = summary.Summary(dataPath + 'annotation.pklz')


def test_run():

	s = summary.Summary(dataPath + 'annotation.pklz')

	s.run(dataPath + "expression", dataPath + "expression_case")

	os.remove('proteome_features.tsv')
	# os.remove('isoform_length.tsv')
	# os.remove('exons.tsv')
	# os.remove('exons_new.tsv')
	# os.remove('structural_features.tsv')
	os.remove("switches_spada.tsv")

def test_proteomeStatistics():

	s = summary.Summary(dataPath + 'annotation.pklz')

	s.proteomeStatistics(dataPath + "expression", dataPath + "expression_case")
	proteome = [ x for x in io.readTable("proteome_features.tsv") ]

	assert len(proteome) == 20
	txs = [ x['Transcript'] for x in proteome if x['Feature_type'] == 'Transcript' ]
	assert len(txs) == len(set(txs))

	# ENSG00.5 is complete, as it only lacks information of its two aberrant transcripts
	assert [ x for x in proteome if x['GeneId'] == 'ENSG00.5' ]

	assert len([ x for x in proteome if x['Feature_type'] == 'Prosite' ]) == 3
	assert len([ x for x in proteome if x['Feature_type'] == 'Pfam' ]) == 3

	# ENST08.1 goes first in the file, and both have same median
	assert len([ x for x in proteome if x['Transcript'] == 'ENST08.1' and x['Feature_type'] != 'Transcript' ]) == 2
	assert len([ x for x in proteome if x['Transcript'] == 'ENST09.1' ]) == 0

	assert len([ x for x in proteome if x['Transcript'] == 'ENST18.3' and x['Feature_type'] != 'Transcript' ]) == 1

	os.remove('proteome_features.tsv')

from spada.io import io
from spada.methods import summary

import os
import pytest

scriptPath = os.path.realpath(__file__)
dataPath = os.path.dirname(scriptPath) + "/../../data/"

def test_init():

	s = summary.Summary(dataPath + 'annotation.pklz')


def test_run():

	s = summary.Summary(dataPath + 'annotation.pklz')

	s.run(dataPath + "expression", dataPath + "expression_case")

	os.remove('proteome_features.tsv')
	# os.remove('isoform_length.tsv')
	# os.remove('exons.tsv')
	# os.remove('exons_new.tsv')
	# os.remove('structural_features.tsv')
	os.remove("switches_spada.tsv")

def test_proteomeStatistics():

	s = summary.Summary(dataPath + 'annotation.pklz')

	s.proteomeStatistics(dataPath + "expression", dataPath + "expression_case")
	proteome = [ x for x in io.readTable("proteome_features.tsv") ]

	assert len(proteome) == 20
	txs = [ x['Transcript'] for x in proteome if x['Feature_type'] == 'Transcript' ]
	assert len(txs) == len(set(txs))

	# ENSG00.5 is complete, as it only lacks information of its two aberrant transcripts
	assert [ x for x in proteome if x['GeneId'] == 'ENSG00.5' ]

	assert len([ x for x in proteome if x['Feature_type'] == 'Prosite' ]) == 3
	assert len([ x for x in proteome if x['Feature_type'] == 'Pfam' ]) == 3

	# ENST08.1 goes first in the file, and both have same median
	assert len([ x for x in proteome if x['Transcript'] == 'ENST08.1' and x['Feature_type'] != 'Transcript' ]) == 2
	assert len([ x for x in proteome if x['Transcript'] == 'ENST09.1' ]) == 0

	assert len([ x for x in proteome if x['Transcript'] == 'ENST18.3' and x['Feature_type'] != 'Transcript' ]) == 1

	os.remove('proteome_features.tsv')
# os.remove('isoform_length.tsv') # os.remove('exons.tsv') # os.remove('exons_new.tsv') # os.remove('structural_features.tsv') # ENSG00.5 is complete, as it only lacks information of its two aberrant transcripts # ENST08.1 goes first in the file, and both have same median