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tests: include preprocessing tests
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@ibludau
ibludau committed Jan 22, 2024
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#!python -m unittest tests.test_utils
"""This module provides unit tests for alphamap.cli."""

# builtin
import unittest

import os
import pandas as pd
import numpy as np
from pyteomics import fasta
import warnings

# local
from alphamap.preprocessing import extract_uniprot_id, \
expand_protein_ids, \
pep_position_helper, \
get_peptide_position, \
get_ptm_sites, \
get_modifications, \
format_input_data

THIS_FOLDER = os.path.dirname(__file__)
TEST_FOLDER = os.path.join(
f"{os.path.dirname(THIS_FOLDER)}",
"nbs",
"testdata",
)

test_df = pd.DataFrame(data={'all_protein_ids': ["A0A024R161;A0A087WT10;A0A087WTH1",
"A0A024R161;A0A087WT10",
"A0A087WTH5","A0A087WTH5",
"Nonsense"],
'modified_sequence': ["PEPT[Phospho (STY)]IDER",
"SEQ[GlyGly (K)]UENCE[GlyGly (K)]R",
"VIEWER","NONSEQ",
"NONSENSE"],
'naked_sequence': ["PEPTIDER",
"SEQUENCER",
"VIEWER","NONSEQ",
"NONSENSE"]})

test_df_expanded = pd.DataFrame(data={'unique_protein_id': ["A0A024R161", "A0A087WT10", "A0A087WTH1",
"A0A024R161", "A0A087WT10",
"A0A087WTH5","A0A087WTH5",
"Nonsense"],
'modified_sequence': ["PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER",
"SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R",
"VIEWER","NONSEQ",
"NONSENSE"],
'naked_sequence': ["PEPTIDER", "PEPTIDER", "PEPTIDER",
"SEQUENCER", "SEQUENCER",
"VIEWER","NONSEQ",
"NONSENSE"],
'all_protein_ids': ["A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1",
"A0A024R161;A0A087WT10", "A0A024R161;A0A087WT10",
"A0A087WTH5","A0A087WTH5",
"Nonsense"]})

test_df_expanded_peptide_position = pd.DataFrame(data={'unique_protein_id': ["A0A024R161", "A0A087WT10", "A0A087WTH1",
"A0A024R161", "A0A087WT10",
"A0A087WTH5"],
'modified_sequence': ["PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER",
"SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R",
"VIEWER"],
'naked_sequence': ["PEPTIDER", "PEPTIDER", "PEPTIDER",
"SEQUENCER", "SEQUENCER",
"VIEWER"],
'all_protein_ids': ["A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1",
"A0A024R161;A0A087WT10", "A0A024R161;A0A087WT10",
"A0A087WTH5"],
'start':[3,28,107,95,150,1],
'end':[10,35,114,103,158,6]})

test_df_modifications = pd.DataFrame(data={'unique_protein_id': ["A0A024R161", "A0A087WT10", "A0A087WTH1",
"A0A024R161", "A0A087WT10",
"A0A087WTH5"],
'modified_sequence': ["PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER", "PEPT[Phospho (STY)]IDER",
"SEQ[GlyGly (K)]UENCE[GlyGly (K)]R", "SEQ[GlyGly (K)]UENCE[GlyGly (K)]R",
"VIEWER"],
'naked_sequence': ["PEPTIDER", "PEPTIDER", "PEPTIDER",
"SEQUENCER", "SEQUENCER",
"VIEWER"],
'all_protein_ids': ["A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1", "A0A024R161;A0A087WT10;A0A087WTH1",
"A0A024R161;A0A087WT10", "A0A024R161;A0A087WT10",
"A0A087WTH5"],
'start':[3,28,107,95,150,1],
'end':[10,35,114,103,158,6],
'PTMsites':[[3],[3],[3],[2,7],[2,7],[]],
'PTMtypes':[["[Phospho (STY)]"],["[Phospho (STY)]"],["[Phospho (STY)]"],["[GlyGly (K)]","[GlyGly (K)]"],["[GlyGly (K)]","[GlyGly (K)]"],[]]})

test_fasta = fasta.IndexedUniProt(os.path.join(TEST_FOLDER,'test.fasta'))

class TestPreprocessing(unittest.TestCase):
def test_extract_uniprot_id(self, ):
prot_id_1 = 'sp|P02769|ALBU_BOVIN'
assert 'P02769' == extract_uniprot_id(prot_id_1)
prot_id_2 = 'CON__P02769'
assert 'P02769' == extract_uniprot_id(prot_id_2)

def test_expand_protein_ids(self, ):
res = expand_protein_ids(test_df)
pd.testing.assert_frame_equal(res,test_df_expanded)

def test_pep_position_helper(self, ):
start, end = pep_position_helper("PEPTIDER","A0A024R161",test_fasta)
np.testing.assert_equal([start, end], [3,10])

def test_get_peptide_position(self, ):
with warnings.catch_warnings(record=True) as w:
res = get_peptide_position(test_df_expanded, test_fasta)
assert len(w) == 2
assert "Peptide sequence NONSEQ could not be mached" in str(w[0].message)
assert "No matching entry for Nonsense" in str(w[1].message)
pd.testing.assert_frame_equal(res,test_df_expanded_peptide_position)

def test_get_ptm_sites(self, ):
myPep = "PEPT[Phospho]IDE[GlyGly (K)]R"
res = get_ptm_sites(myPep, modification_reg=r'\[.*?\]')
np.testing.assert_equal(res, [3,6])
myPep = "[Ac]PEPTIDE[GlyGly (K)]R"
res = get_ptm_sites(myPep, modification_reg=r'\[.*?\]')
np.testing.assert_equal(res, [0,6])

def test_get_modifications(self, ):
res = get_modifications(test_df_expanded_peptide_position, mod_reg = r'\[.*?\]')
pd.testing.assert_frame_equal(res, test_df_modifications)

def test_format_input_data(self, ):
with warnings.catch_warnings(record=True) as w:
res = format_input_data(df=test_df, fasta = test_fasta, modification_exp = r'\[.*?\]')
assert len(w) == 2
assert "Peptide sequence NONSEQ could not be mached" in str(w[0].message)
assert "No matching entry for Nonsense" in str(w[1].message)
pd.testing.assert_frame_equal(res, test_df_modifications)

if __name__ == "__main__":
unittest.main()

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