<reponame>white-lab/pyproteome<filename>tests/brainrnaseq_test.py
from unittest import TestCase

import brainrnaseq as brs

import pandas as pd


class BrainRNASeqTest(TestCase):
    def test_mapping_data(self):
        items = {
            'Homo sapiens': ['A1BG', 'A1B|ABG|GAB|HYST2477', '16S rRNA', '-'],
            'Mus musculus': ['Pzp', 'A1m|A2m|AI893533|MAM', 'ND2', '-'],
        }

        for species, vals in items.items():
            for _ in range(2):
                map = brs.cache.get_mapping_data(
                    species=species,
                )

                self.assertIsInstance(
                    map,
                    pd.DataFrame,
                )
                self.assertEqual(
                    map.index[0],
                    vals[0],
                )
                self.assertEqual(
                    map.iloc[0]['Synonyms'],
                    vals[1],
                )
                self.assertEqual(
                    map.index[-1],
                    vals[2],
                )
                self.assertEqual(
                    map.iloc[-1]['Synonyms'],
                    vals[3],
                )

            map = brs.cache.get_mapping_data(
                species=species,
                force=True,
            )
            self.assertIsInstance(
                map,
                pd.DataFrame,
            )

    def test_mapping(self):
        for _ in range(2):
            for gene in ['Jak2', 'Fd17']:
                self.assertEqual(
                    brs.mapping.get_symbol_mapping(
                        gene=gene,
                        species='Mus musculus',
                    ),
                    'Jak2',
                )

            self.assertEqual(
                brs.mapping.get_symbol_mapping(
                    gene='NaNNaNNaN',
                    species='Mus musculus',
                ),
                None,
            )

            for gene in ['JAK2', 'JTK10', 'THCYT3']:
                self.assertEqual(
                    brs.mapping.get_symbol_mapping(
                        gene=gene,
                        species='Homo sapiens',
                    ),
                    'JAK2',
                )

            # Ambiguous gene
            self.assertEqual(
                brs.mapping.get_symbol_mapping(
                    gene='AP-1',
                    species='Homo sapiens',
                ),
                'FOS',
            )

    def test_barres_seq_data(self):
        brs.cache.get_barres_seq_data()

        items = {
            'Homo sapiens': ['Gene', '1/2-SBSRNA4', 'ZZZ3'],
            'Mus musculus': ['gene', '0610005C13Rik', 'Zzz3'],
        }

        for species, (col, first, last) in items.items():
            self.assertEqual(
                brs.cache.BARRES_SPECIES_DATA[species].iloc[0][col],
                first,
            )
            self.assertEqual(
                brs.cache.BARRES_SPECIES_DATA[species].iloc[-1][col],
                last,
            )

    def test_hansen_seq_data(self):
        brs.cache.get_hansen_seq_data()

        items = {
            'Homo sapiens': ['A1BG', 'SCO2'],
            'Mus musculus': ['A1bg', 'Sco2'],
        }

        for species, (first, last) in items.items():
            self.assertEqual(
                brs.cache.HANSEN_SPECIES_DATA[species].index[0],
                first,
            )
            self.assertEqual(
                brs.cache.HANSEN_SPECIES_DATA[species].index[-1],
                last,
            )

    def test_barres_enrichment_table(self):
        tab = brs.enrichments.build_barres_table()

        self.assertIsInstance(
            tab,
            dict,
        )

    def test_hansen_enrichment_table(self):
        tab = brs.enrichments.build_hansen_table()

        self.assertIsInstance(
            tab,
            dict,
        )

    def test_barres_enrichments(self):
        items = {
            'Homo sapiens': {
                'AGT': 'Astrocyte',
                'GFAP': 'Astrocyte',
                'IDI2-AS1': 'Astrocyte',
                'CD34': 'Endothelia',
                'RNU11': 'Endothelia',
                'CCL3L1': 'Microglia',
                'CD33': 'Microglia',
                'INPP5D': 'Microglia',
                'SIGLEC5': 'Microglia',
                'SIGLEC8': 'Microglia',
                'SIGLEC9': 'Microglia',
                'SIGLEC10': 'Microglia',
                'SIGLEC14': 'Microglia',
                'FOLH1': 'Myelinating Oligodendrocytes',
                'CD22': 'Myelinating Oligodendrocytes',
                'MAG': 'Myelinating Oligodendrocytes',
                'GAD2': 'Neuron',
                'SYT4': 'Neuron',
            },
            'Mus musculus': {
                'Sumo2': 'Astrocyte',
                'AU021092': 'Endothelia',
                'OncoM': 'Microglia',
                'Siglec-1': 'Microglia',
                'Siglec1': 'Microglia',
                'Cd22': 'Microglia',
                'Cd33': 'Microglia',
                'Siglec-3': 'Microglia',
                'mSiglec-E': 'Microglia',
                'Siglece': 'Microglia',
                'Siglec5': 'Microglia',
                'Siglec9': 'Microglia',
                'Siglec-H': 'Microglia',
                'Siglecl1': 'Microglia',
                'Siglec12': 'Microglia',
                'siglec-4a': 'Myelinating Oligodendrocytes',
                'Otm': 'Myelinating Oligodendrocytes',
                'Reln': 'Neuron',
            },
        }
        for species, vals in items.items():
            enrich = brs.enrichments.get_enrichments(
                species=species,
                backend='Barres',
            )

            self.assertIsInstance(
                enrich,
                dict,
            )
            for key, val in vals.items():
                if key not in enrich:
                    print(key)
                    continue
                self.assertEqual(
                    enrich[key],
                    val,
                )

    def test_hansen_enrichments(self):
        items = {
            'Homo sapiens': {
                'AGT': 'Astrocyte',
                'CD34': 'Endothelia',
                'FOLH1': 'Myelinating Oligodendrocytes',
                'GAD2': 'Neuron',
                'SYT4': 'Neuron',
            },
            'Mus musculus': {
                'AU021092': 'Endothelia',
                'OncoM': 'Microglia',
                'mSiglec-E': 'Microglia',
                'Siglece': 'Microglia',
                'Siglec5': 'Microglia',
                'Siglec9': 'Microglia',
                'Siglecl1': 'Microglia',
                'Siglec12': 'Microglia',
                'siglec-4a': 'Myelinating Oligodendrocytes',
                'Otm': 'Myelinating Oligodendrocytes',
                'Reln': 'Neuron',
            },
        }
        for species, vals in items.items():
            enrich = brs.enrichments.get_enrichments(
                species=species,
                backend='Hansen',
            )

            self.assertIsInstance(
                enrich,
                dict,
            )
            for key, val in vals.items():
                if key not in enrich:
                    print(key)
                    continue
                self.assertEqual(
                    enrich[key],
                    val,
                )

from unittest import TestCase

import brainrnaseq as brs

import pandas as pd


class BrainRNASeqTest(TestCase):
    def test_mapping_data(self):
        items = {
            'Homo sapiens': ['A1BG', 'A1B|ABG|GAB|HYST2477', '16S rRNA', '-'],
            'Mus musculus': ['Pzp', 'A1m|A2m|AI893533|MAM', 'ND2', '-'],
        }

        for species, vals in items.items():
            for _ in range(2):
                map = brs.cache.get_mapping_data(
                    species=species,
                )

                self.assertIsInstance(
                    map,
                    pd.DataFrame,
                )
                self.assertEqual(
                    map.index[0],
                    vals[0],
                )
                self.assertEqual(
                    map.iloc[0]['Synonyms'],
                    vals[1],
                )
                self.assertEqual(
                    map.index[-1],
                    vals[2],
                )
                self.assertEqual(
                    map.iloc[-1]['Synonyms'],
                    vals[3],
                )

            map = brs.cache.get_mapping_data(
                species=species,
                force=True,
            )
            self.assertIsInstance(
                map,
                pd.DataFrame,
            )

    def test_mapping(self):
        for _ in range(2):
            for gene in ['Jak2', 'Fd17']:
                self.assertEqual(
                    brs.mapping.get_symbol_mapping(
                        gene=gene,
                        species='Mus musculus',
                    ),
                    'Jak2',
                )

            self.assertEqual(
                brs.mapping.get_symbol_mapping(
                    gene='NaNNaNNaN',
                    species='Mus musculus',
                ),
                None,
            )

            for gene in ['JAK2', 'JTK10', 'THCYT3']:
                self.assertEqual(
                    brs.mapping.get_symbol_mapping(
                        gene=gene,
                        species='Homo sapiens',
                    ),
                    'JAK2',
                )

            # Ambiguous gene
            self.assertEqual(
                brs.mapping.get_symbol_mapping(
                    gene='AP-1',
                    species='Homo sapiens',
                ),
                'FOS',
            )

    def test_barres_seq_data(self):
        brs.cache.get_barres_seq_data()

        items = {
            'Homo sapiens': ['Gene', '1/2-SBSRNA4', 'ZZZ3'],
            'Mus musculus': ['gene', '0610005C13Rik', 'Zzz3'],
        }

        for species, (col, first, last) in items.items():
            self.assertEqual(
                brs.cache.BARRES_SPECIES_DATA[species].iloc[0][col],
                first,
            )
            self.assertEqual(
                brs.cache.BARRES_SPECIES_DATA[species].iloc[-1][col],
                last,
            )

    def test_hansen_seq_data(self):
        brs.cache.get_hansen_seq_data()

        items = {
            'Homo sapiens': ['A1BG', 'SCO2'],
            'Mus musculus': ['A1bg', 'Sco2'],
        }

        for species, (first, last) in items.items():
            self.assertEqual(
                brs.cache.HANSEN_SPECIES_DATA[species].index[0],
                first,
            )
            self.assertEqual(
                brs.cache.HANSEN_SPECIES_DATA[species].index[-1],
                last,
            )

    def test_barres_enrichment_table(self):
        tab = brs.enrichments.build_barres_table()

        self.assertIsInstance(
            tab,
            dict,
        )

    def test_hansen_enrichment_table(self):
        tab = brs.enrichments.build_hansen_table()

        self.assertIsInstance(
            tab,
            dict,
        )

    def test_barres_enrichments(self):
        items = {
            'Homo sapiens': {
                'AGT': 'Astrocyte',
                'GFAP': 'Astrocyte',
                'IDI2-AS1': 'Astrocyte',
                'CD34': 'Endothelia',
                'RNU11': 'Endothelia',
                'CCL3L1': 'Microglia',
                'CD33': 'Microglia',
                'INPP5D': 'Microglia',
                'SIGLEC5': 'Microglia',
                'SIGLEC8': 'Microglia',
                'SIGLEC9': 'Microglia',
                'SIGLEC10': 'Microglia',
                'SIGLEC14': 'Microglia',
                'FOLH1': 'Myelinating Oligodendrocytes',
                'CD22': 'Myelinating Oligodendrocytes',
                'MAG': 'Myelinating Oligodendrocytes',
                'GAD2': 'Neuron',
                'SYT4': 'Neuron',
            },
            'Mus musculus': {
                'Sumo2': 'Astrocyte',
                'AU021092': 'Endothelia',
                'OncoM': 'Microglia',
                'Siglec-1': 'Microglia',
                'Siglec1': 'Microglia',
                'Cd22': 'Microglia',
                'Cd33': 'Microglia',
                'Siglec-3': 'Microglia',
                'mSiglec-E': 'Microglia',
                'Siglece': 'Microglia',
                'Siglec5': 'Microglia',
                'Siglec9': 'Microglia',
                'Siglec-H': 'Microglia',
                'Siglecl1': 'Microglia',
                'Siglec12': 'Microglia',
                'siglec-4a': 'Myelinating Oligodendrocytes',
                'Otm': 'Myelinating Oligodendrocytes',
                'Reln': 'Neuron',
            },
        }
        for species, vals in items.items():
            enrich = brs.enrichments.get_enrichments(
                species=species,
                backend='Barres',
            )

            self.assertIsInstance(
                enrich,
                dict,
            )
            for key, val in vals.items():
                if key not in enrich:
                    print(key)
                    continue
                self.assertEqual(
                    enrich[key],
                    val,
                )

    def test_hansen_enrichments(self):
        items = {
            'Homo sapiens': {
                'AGT': 'Astrocyte',
                'CD34': 'Endothelia',
                'FOLH1': 'Myelinating Oligodendrocytes',
                'GAD2': 'Neuron',
                'SYT4': 'Neuron',
            },
            'Mus musculus': {
                'AU021092': 'Endothelia',
                'OncoM': 'Microglia',
                'mSiglec-E': 'Microglia',
                'Siglece': 'Microglia',
                'Siglec5': 'Microglia',
                'Siglec9': 'Microglia',
                'Siglecl1': 'Microglia',
                'Siglec12': 'Microglia',
                'siglec-4a': 'Myelinating Oligodendrocytes',
                'Otm': 'Myelinating Oligodendrocytes',
                'Reln': 'Neuron',
            },
        }
        for species, vals in items.items():
            enrich = brs.enrichments.get_enrichments(
                species=species,
                backend='Hansen',
            )

            self.assertIsInstance(
                enrich,
                dict,
            )
            for key, val in vals.items():
                if key not in enrich:
                    print(key)
                    continue
                self.assertEqual(
                    enrich[key],
                    val,
                )
# Ambiguous gene