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Commit ddf4a2a6 authored by Nicolas MAILLET's avatar Nicolas MAILLET
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Increase global coverage and test for parallel functions

parent aceef805
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tests/test_core.py
View file @ ddf4a2a6
"""Tests for core.py"""
import gzip
import pytest
from .context import rpg
from rpg import core
......@@ -175,6 +176,44 @@ def test_output_results(capsys, tmpdir):
"al peptide: WQSD\nC terminal peptide: F\n" + \
output_file.read()
# No output file
output_file = None
fmt = "csv"
quiet = False
verbose = 3
core.output_results(output_file, all_seq_digested, fmt, quiet,
verbose)
out, err = capsys.readouterr()
assert out == "\nNumber of cleavage: 4\nCleavage position: 4, 7, 12, 15\n"\
"Number of miscleavage: 0\nmiscleavage position: \nmis"\
"cleavage ratio: 0.00%\nSmallest peptide size: 1\nN termin"\
"al peptide: WQSD\nC terminal peptide: F\nOriginal_header,"\
"No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.52598,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.29758,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.48938,3."\
"14,FZQSD\nInput,3,fake_enzyme1,15,3,349.297"\
"58,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"19188,5.97,F\n"
# No output file et less verbose
output_file = None
fmt = "csv"
quiet = False
verbose = 1
core.output_results(output_file, all_seq_digested, fmt, quiet,
verbose)
out, err = capsys.readouterr()
assert out == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.52598,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.29758,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.48938,3."\
"14,FZQSD\nInput,3,fake_enzyme1,15,3,349.297"\
"58,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"19188,5.97,F\n"
def test_peptide():
"""Test class 'Peptide'"""
header = "Test"
......@@ -216,3 +255,79 @@ def test_peptide():
# Test function 'def get_isoelectric_point():'
assert pep3.get_isoelectric_point() == 2.91
def test_next_read(capsys, tmpdir):
""" Test function 'next_read(files)'"""
# Test fasta (multi-line) file with two sequences
fasta_file = tmpdir.join("test.fasta")
fasta_file.write(">Fake1\nACGTTATATGCTA\nTGTG\n>Fake2\nCAGTACTAGCA")
# Only a portion of the file (from 0 to 3)
res = core.next_read(fasta_file, 0, 3)
# First read
a_read = next(res, None)
assert a_read == (">Fake1", "ACGTTATATGCTATGTG")
# No second read
a_read = next(res, None)
assert a_read is None
# Full file
res = core.next_read(fasta_file, 0, 35)
# First read
a_read = next(res, None)
assert a_read == (">Fake1", "ACGTTATATGCTATGTG")
# No second read
a_read = next(res, None)
assert a_read == (">Fake2", "CAGTACTAGCA")
# Test gzipped fasta file
data = b">Fake1\nACGTTATATGCTATGT\n"
fastagz_file = tmpdir.join("test.fasta.gz")
with gzip.open(fastagz_file, "wb") as fil:
fil.write(data)
res = core.next_read(fastagz_file, 0, 35)
# First read
a_read = next(res)
assert a_read == (">Fake1", "ACGTTATATGCTATGT")
# Test fastq file with two sequence
fastq_file = tmpdir.join("test.fastq")
fastq_file.write("@Fake1\nACGTTATATGCTATGTG\n+Fake1\n5Q8D8=64DS-+DZ84!\n"\
"@Fake2\nATGCATGCTG\n+Fake1\n8173*8173!")
# First sequence only (from 0 to 3)
res = core.next_read(fastq_file, 0, 3)
# First read
a_read = next(res, None)
assert a_read == ("@Fake1", "ACGTTATATGCTATGTG")
# No second read
a_read = next(res, None)
assert a_read is None
# Full file
res = core.next_read(fastq_file, 0, 1000)
# First read
a_read = next(res, None)
assert a_read == ("@Fake1", "ACGTTATATGCTATGTG")
# Second read
a_read = next(res, None)
assert a_read == ("@Fake2", "ATGCATGCTG")
# Test gzipped fastq file
data = b"@Fake1\nACGTTATATGCTATGTG\n+Fake1\n5Q8D8=64DS-+DZ84!\n"
fastqgz_file = tmpdir.join("test.fastq.gz")
with gzip.open(fastqgz_file, "wb") as fil:
fil.write(data)
res = core.next_read(fastqgz_file, 0, 35)
# First read
a_read = next(res)
assert a_read == ("@Fake1", "ACGTTATATGCTATGTG")
# Test wrong gzipped fastq file
data = b"+Fake1\nACGTTATATGCTATGTG\n+Fake1\n5Q8D8=64DS-+DZ84!\n"
fastqgz_file = tmpdir.join("test.fastq.gz")
with gzip.open(fastqgz_file, "wb") as fil:
fil.write(data)
with pytest.raises(ValueError) as pytest_wrapped_e:
res = core.next_read(fastqgz_file, 0, 35)
a_read = next(res)
assert pytest_wrapped_e.type == ValueError
assert str(pytest_wrapped_e.value) == "input file format not recognized (+)."
tests/test_digest.py
View file @ ddf4a2a6
......@@ -53,6 +53,7 @@ def test_resultonedigestion():
assert res_dig0 != res_dig3
assert res_dig0 != res_dig4
assert res_dig0 != res_dig5
assert res_dig0 != 42
# Test function '__format__()'
format_res = res_dig0.__format__("csv")
......@@ -171,7 +172,7 @@ def test_one_digest():
assert res.peptides[0].__repr__() == res_pep0.__repr__()
assert res.peptides[1].__repr__() == res_pep1.__repr__()
def test_digest_one_sequence():
def test_digest_one_sequence(capsys):
"""Test function 'def digest_one_sequence(seq, enz, mode)'"""
enzymes = []
# First enzyme: cut after D not precedeed by S
......@@ -248,6 +249,8 @@ def test_digest_one_sequence():
assert res[1].peptides[1].__repr__() == res_pep2.__repr__()
assert res[1].peptides[2].__repr__() == res_pep3.__repr__()
capsys.readouterr()
def test_sequential_digest():
"""Test function 'sequential_digest(seq, enz)'"""
enzymes = []
......@@ -330,7 +333,8 @@ def test_concurrent_digest():
assert res[0].peptides[4].__repr__() == res_pep4.__repr__()
def test_digest_from_input(capsys, tmpdir):
""" Test function 'digest_from_input(input_data, enzymes, mode)'"""
""" Test function 'digest_from_input(input_data, input_type, enz,
mode, aa_pka, nb_proc=1)'"""
rule_dict = {}
rule_txt = "(S)(D,)"
rule_dict[rule_txt] = True
......@@ -346,7 +350,6 @@ def test_digest_from_input(capsys, tmpdir):
enzymes, mode, aa_pka)
_, err = capsys.readouterr()
assert err == "Input Error: input file format not recognized (f).\n"
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 1
# Test input data
......@@ -377,6 +380,14 @@ def test_digest_from_input(capsys, tmpdir):
": 165.19188\npKa values from: IPC\nPep. p"\
"I: 5.97\nSequence: F\n]\n"
# Test wrong input data
with pytest.raises(SystemExit) as pytest_wrapped_e:
seq = "WQSD2ESD"
res = digest.digest_from_input(seq, "sequence", enzymes, mode, aa_pka)
_, err = capsys.readouterr()
assert err == "Input Error: amino acid \"2\" in WQSD2ESD not recognized.\n"
assert pytest_wrapped_e.value.code == 1
# Test fasta file
fasta_file = tmpdir.join("test.fasta")
fasta_file.write(">Fake1\nWQSDESDFZQS\nDESDF\n>Fake2\nNPHARDORCOMPLET")
......@@ -415,41 +426,113 @@ def test_digest_from_input(capsys, tmpdir):
" IPC\nPep. pI: 7.16\nSequence: NPHARDORCO"\
"MPLET\n]\n"
# Test fastq file (same result)
# Test fastq file (same result) with multiple proc
fastq_file = tmpdir.join("test.fastq")
fastq_file.write("@Fake1\nWQSDESDFZQSDESDF\n+Fake1\nnWQSDESDFZQSDESDF\n@F"\
"ake2\nNPHARDORCOMPLET\n+Fake2\nnNPHARDORCOMPLET\n")
res = digest.digest_from_input(str(fastq_file), "file", enzymes, mode,
aa_pka)
assert res[0][0].__repr__() == "Number of cleavage: 4\nNumber of miscle"\
"avage: 0\nPositions of miscleavage: []"\
"\nRatio of miscleavage: 0.0\nPeptides: "\
"[Original header: Fake1\nNo. peptide: 0\n"\
"Enzyme: fake_enzyme1\nCleav. pos: 4\nPep."\
" size: 4\nPep. mass: 534.52598\npKa value"\
"s from: IPC\nPep. pI: 3.14\nSequence: WQS"\
"D\n, Original header: Fake1\nNo. peptide:"\
" 1\nEnzyme: fake_enzyme1\nCleav. pos: 7\n"\
"Pep. size: 3\nPep. mass: 349.29758\npKa v"\
"alues from: IPC\nPep. pI: 3.04\nSequence:"\
" ESD\n, Original header: Fake1\nNo. pepti"\
"de: 2\nEnzyme: fake_enzyme1\nCleav. pos: "\
"12\nPep. size: 5\nPep. mass: 495.48938\np"\
"Ka values from: IPC\nPep. pI: 3.14\nSeque"\
"nce: FZQSD\n, Original header: Fake1\nNo."\
" peptide: 3\nEnzyme: fake_enzyme1\nCleav."\
" pos: 15\nPep. size: 3\nPep. mass: 349.29"\
"758\npKa values from: IPC\nPep. pI: 3.04"\
"\nSequence: ESD\n, Original header: Fake1"\
"\nNo. peptide: 4\nEnzyme: fake_enzyme1\nC"\
"leav. pos: 16\nPep. size: 1\nPep. mass: 1"\
"65.19188\npKa values from: IPC\nPep. pI: "\
"5.97\nSequence: F\n]\n"
assert res[1][0].__repr__() == "Number of cleavage: 0\nNumber of miscle"\
"avage: 0\nPositions of miscleavage: []"\
"\nRatio of miscleavage: 0\nPeptides: [O"\
"riginal header: Fake2\nNo. peptide: 0\nEn"\
"zyme: fake_enzyme1\nCleav. pos: 0\nPep. s"\
"ize: 15\nPep. mass: 2014.35098\npKa value"\
"s from: IPC\nPep. pI: 7.16\nSequence: NPH"\
"ARDORCOMPLET\n]\n"
aa_pka, 2)
# Multi proc, we an't predict which result will be first or second
results_unsorted = []
results_unsorted.append("Number of cleavage: 4\nNumber of miscle"\
"avage: 0\nPositions of miscleavage: []"\
"\nRatio of miscleavage: 0.0\nPeptides: "\
"[Original header: Fake1\nNo. peptide: 0\n"\
"Enzyme: fake_enzyme1\nCleav. pos: 4\nPep."\
" size: 4\nPep. mass: 534.52598\npKa value"\
"s from: IPC\nPep. pI: 3.14\nSequence: WQS"\
"D\n, Original header: Fake1\nNo. peptide:"\
" 1\nEnzyme: fake_enzyme1\nCleav. pos: 7\n"\
"Pep. size: 3\nPep. mass: 349.29758\npKa v"\
"alues from: IPC\nPep. pI: 3.04\nSequence:"\
" ESD\n, Original header: Fake1\nNo. pepti"\
"de: 2\nEnzyme: fake_enzyme1\nCleav. pos: "\
"12\nPep. size: 5\nPep. mass: 495.48938\np"\
"Ka values from: IPC\nPep. pI: 3.14\nSeque"\
"nce: FZQSD\n, Original header: Fake1\nNo."\
" peptide: 3\nEnzyme: fake_enzyme1\nCleav."\
" pos: 15\nPep. size: 3\nPep. mass: 349.29"\
"758\npKa values from: IPC\nPep. pI: 3.04"\
"\nSequence: ESD\n, Original header: Fake1"\
"\nNo. peptide: 4\nEnzyme: fake_enzyme1\nC"\
"leav. pos: 16\nPep. size: 1\nPep. mass: 1"\
"65.19188\npKa values from: IPC\nPep. pI: "\
"5.97\nSequence: F\n]\n")
results_unsorted.append("Number of cleavage: 0\nNumber of miscle"\
"avage: 0\nPositions of miscleavage: []"\
"\nRatio of miscleavage: 0\nPeptides: [O"\
"riginal header: Fake2\nNo. peptide: 0\nEn"\
"zyme: fake_enzyme1\nCleav. pos: 0\nPep. s"\
"ize: 15\nPep. mass: 2014.35098\npKa value"\
"s from: IPC\nPep. pI: 7.16\nSequence: NPH"\
"ARDORCOMPLET\n]\n")
assert len(res) == 2
assert res[0][0].__repr__() in results_unsorted
assert res[1][0].__repr__() in results_unsorted
# Test wrong fastq file
fastq_file = tmpdir.join("test.fastq")
fastq_file.write("?Fake1\nWQSDESDFZQSDESDF\n+Fake1\nnWQSDESDFZQSDESDF\n@F"\
"ake2\nNPHARDORCOMPLET\n+Fake2\nnNPHARDORCOMPLET\n")
with pytest.raises(SystemExit) as pytest_wrapped_e:
res = digest.digest_from_input(str(fastq_file), "file", enzymes, mode,
aa_pka, 4)
_, err = capsys.readouterr()
assert err == "Input Error: input file format not recognized (?).\n"
assert pytest_wrapped_e.value.code == 1
# Test wrong input type
with pytest.raises(SystemExit) as pytest_wrapped_e:
res = digest.digest_from_input(str(fastq_file), "42", enzymes, mode,
aa_pka, 4)
_, err = capsys.readouterr()
assert err == "Input Error: input type not recognized (42).\n"
assert pytest_wrapped_e.value.code == 1
def test_digest_part(tmpdir):
""" Test function 'digest_part(offset_start, offset_end, file, enz,
mode, aa_pka)'"""
# Fake input file
file = tmpdir.join("test.fasta")
file.write(">Fake1\nWQSDESDFZQS\nDESDF\n>Fake2\nNPHARDORCOMPLET")
rule_dict = {}
rule_txt = "(S)(D,)"
rule_dict[rule_txt] = True
all_rules = rule.create_rules(rule_dict)
enz1 = enzyme.Enzyme(-1, "fake_enzyme1", all_rules)
enz = [enz1]
mode = "sequential"
aa_pka = core.AA_PKA_IPC
# Read the whole file
offset_start = 0
offset_end = 1000
# Get the queries
results_digestion = digest.digest_part(offset_start, offset_end, file, enz,
mode, aa_pka)
# We have 2 res, one for each ref
assert len(results_digestion) == 2
assert results_digestion[1][0].enzyme_name == "fake_enzyme1"
assert results_digestion[1][0].nb_cleavage == 0
# Fake false input file
file = tmpdir.join("test.fasta")
file.write(",Fake1\nWQSDESDFZQS\nDESDF\n>Fake2\nNPHARDORCOMPLET")
rule_dict = {}
rule_txt = "(S)(D,)"
rule_dict[rule_txt] = True
all_rules = rule.create_rules(rule_dict)
enz1 = enzyme.Enzyme(-1, "fake_enzyme1", all_rules)
enz = [enz1]
mode = "sequential"
aa_pka = core.AA_PKA_IPC
# Read the whole file
offset_start = 0
offset_end = 1000
# Get the queries
with pytest.raises(ValueError) as pytest_wrapped_e:
results_digestion = digest.digest_part(offset_start, offset_end, file,
enz, mode, aa_pka)
# We have a ValueError
assert pytest_wrapped_e.type == ValueError
assert str(pytest_wrapped_e.value) == "input file format not recognized (,)."
tests/test_enzyme.py
View file @ ddf4a2a6
......@@ -39,6 +39,7 @@ def test_enzyme(tmpdir):
# Test function '__eq__()'
assert enz0 == enz1
assert enz0 != enz2
assert enz0 != 42
"""Test function
'write_enzyme_in_user_file(self, enz_file=DEFUSERENZFILE)'
......@@ -61,7 +62,7 @@ def test_enzyme(tmpdir):
's\nAVAILABLE_ENZYMES_USER.append(ENZYME)\nC'\
'PT_ENZ += 1\n'
def test_check_enzyme_name():
def test_check_enzyme_name(capsys):
"""Test function 'check_enzyme_name(name_new_enz, all_name_enz)'."""
# Already taken names
......@@ -90,21 +91,4 @@ def test_check_enzyme_name():
res = enzyme.check_enzyme_name(seq_name, all_name)
assert res is False
'''
def test_user_creation_enzyme(capsys, monkeypatch):
"""Test function 'user_creation_enzyme()'"""
monkeypatch.setattr(builtins.input, "Mark")
i = input("What is your name?")
assert i == "Mark"
inputs = [10, 'y']
input_generator = (i for i in inputs)
monkeypatch.setitem('__builtins__.input', lambda prompt: next(input_generator))
core.user_creation_enzyme()
out, err = capsys.readouterr()
print(out)
print(err)
assert input('how many?') == 10
assert input('you sure?') == 'y'
'''
capsys.readouterr()
tests/test_rule.py
View file @ ddf4a2a6
......@@ -87,7 +87,7 @@ def test_rule():
'leaves before D, followed by Q, except...\nD_0.rules.appen'\
'd(D_0Q2)\nENZ.append(D_0)\n\n'
def test_check_rule():
def test_check_rule(capsys):
"""Test function 'check_rule(exprule)'."""
# Good
expr = "(,A or B,)"
......@@ -215,6 +215,8 @@ def test_check_rule():
res = rule.check_rule(expr)
assert res == expr
capsys.readouterr()
def test_split_complex_rule():
"""Test function 'split_complex_rule(rule)'."""
# No 'or'
......@@ -307,7 +309,6 @@ def test_create_rules():
all_rules = {}
# Simplest rule
# cleavage before A
rule1 = "(,A)"
all_rules[rule1] = True
# Truth for this rule
......@@ -375,7 +376,7 @@ def test_create_rules():
assert len(res) == 7
# Double comma and 'or'
# Cleaves after I or J, except if K is after, but cleaves if a L is before
# Cleaves before or after I or J, except if K is after, but cleaves if a L is before
all_rules = {}
rule6 = "(,I or J,)"
all_rules[rule6] = True
......@@ -402,6 +403,20 @@ def test_create_rules():
assert truth6_4 in res
assert len(res) == 4
# Similar complexe rule
# Cleaves before G if there is a H after
# But don't cleaves before G otherwise
all_rules = {}
rule7 = "(,G)(H)"
all_rules[rule7] = True
# Truth for rule7
truth7_1 = rule.Rule(1, "H", True, -1)
truth7 = rule.Rule(0, "G", False, 0) # Don't cleaves after G
truth7.rules.append(truth7_1)
res = rule.create_rules(all_rules)
assert truth7 in res
assert len(res) == 1
def test_handle_rule():
"""Test function 'handle_rule(seq, pos, a_rule, cleavage)'"""
......
tests/test_sequence.py
View file @ ddf4a2a6
"""Tests for sequence.py"""
import pytest
from .context import rpg
from rpg import core
from rpg import sequence
def test_peptide():
"""Test class 'Peptide'"""
header = "fake_sequence"
seq = "QWSDESDF"
enz_name = "Pwet"
aa_pka = core.AA_PKA_IPC
nb_peptide = 42
pep0 = sequence.Peptide(header, seq, enz_name, aa_pka, nb_peptide)
# Test function '__repr__()'
assert pep0.__repr__() == "Original header: fake_sequence\nNo. peptide: "\
"42\nEnzyme: Pwet\nCleav. pos: 0\nPep. size: 8"\
"\nPep. mass: 1012.98488\npKa values from: IPC"\
"\nPep. pI: 2.91\nSequence: QWSDESDF\n"
header = "fake_sequence"
seq = "QWSDESDF"
enz_name = "Pwet"
aa_pka = core.AA_PKA_IPC
nb_peptide = 42
pep1 = sequence.Peptide(header, seq, enz_name, aa_pka, nb_peptide)
header = "fake_sequence"
seq = "QWSDESDW"
enz_name = "Pwet"
aa_pka = core.AA_PKA_IPC
nb_peptide = 42
pep2 = sequence.Peptide(header, seq, enz_name, aa_pka, nb_peptide)
assert pep0 == pep1
assert pep0 != pep2
assert pep0 != 42
def test_sequence():
"""Test class 'Sequence'"""
header = "fake_sequence"
......@@ -28,6 +62,7 @@ def test_sequence():
assert seq0 == seq1
assert seq0 != seq2
assert seq0 != seq3
assert seq0 != 42
def test_check_sequence(capsys):
""" Test function 'check_sequence(seq)'"""
......@@ -35,10 +70,7 @@ def test_check_sequence(capsys):
assert sequence.check_sequence("aiHZODHUoh") == "AIHZODHUOH"
# Bad symbol
with pytest.raises(SystemExit) as pytest_wrapped_e:
with pytest.raises(ValueError) as pytest_wrapped_e:
sequence.check_sequence("a%HZODHUoh")
_, err = capsys.readouterr()
assert err == "Sequence Error: amino acid \"%\" in A%HZODHUOH not recogni"\
"zed.\n"
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 1
assert "amino acid \"%\" in A%HZODHUOH not "\
"recognized." in str(pytest_wrapped_e.value)
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