From 1122fe4df97ea5c0830a457724a1212716c844dd Mon Sep 17 00:00:00 2001
From: Nico Maillet <nicolas.maillet@pasteur.fr>
Date: Wed, 22 Feb 2023 11:55:05 +0100
Subject: [PATCH] Add theoritical peptides functions and firsts tests
---
rpg/RapidPeptidesGenerator.py | 48 ++++++++++++++-
rpg/digest.py | 57 ++++++++++++++++++
rpg/enzyme.py | 48 ++++++++++-----
tests/test_digest.py | 4 ++
tests/test_enzyme.py | 80 +++++++++++++++++++++++--
tests/test_functional.py | 107 ++++++++++++++++++++++++++++++----
6 files changed, 313 insertions(+), 31 deletions(-)
diff --git a/rpg/RapidPeptidesGenerator.py b/rpg/RapidPeptidesGenerator.py
index 667326c..4204a5a 100644
--- a/rpg/RapidPeptidesGenerator.py
+++ b/rpg/RapidPeptidesGenerator.py
@@ -73,6 +73,27 @@ def restricted_float(mc_val):
core.handle_errors("miscleavage value should be a float between 0 "\
"and 100.", 0, "Type ")
+def restricted_int(mc_val):
+ """Restricts input miscleavage value to a int.
+
+ :param mc_val: value to test
+ :type mc_val: int
+
+ :return: the inputed value if correct
+ :rtype: int
+
+ :raises custom TypeError: if value is not an int
+ """
+ try:
+ mc_val = int(mc_val)
+ if mc_val < 0 :
+ core.handle_errors("miscleavage value should be greater then 0.", 0, "Value ")
+ return mc_val
+ except ValueError:
+ # Throw an error
+ core.handle_errors("miscleavage value should be an integer.", 0,
+ "Type ")
+
def restricted_enzyme_id(enz_id):
"""Restrict input enzyme id to a str corresponding to an enzyme.
@@ -204,6 +225,7 @@ def get_enzymes_to_use(mode, id_enz_selected, miscleavage):
mc_enz_inputed)
# Return Enzymes to use
return enzymes_to_use
+
# Not tested
def main():
"""Launcher of RapidPeptidesGenerator"""
@@ -258,12 +280,20 @@ def main():
group_launch.add_argument("-s", "--sequence", metavar="",
help="Input a single protein sequence without "\
"commentary")
- parser.add_argument("-m", "--miscleavage", metavar="", default=[],
+ group_mc = parser.add_mutually_exclusive_group(required=False)
+ group_mc.add_argument("-m", "--miscleavage", metavar="", default=[],
nargs='+', type=restricted_float,
help="Percentage of miscleavage, between 0 and 100,"
" by enzyme(s). It should be in the same order than "
"-enzymes options (e.g. -m 15 5 10). Only for sequenti"
"al digestion (default: 0)")
+ group_mc.add_argument("-t", "--theoretical", metavar="", default=[],
+ nargs='+', type=restricted_int,
+ help="Maximum number of miscleavages, by enzyme(s). "
+ "RPG will produce all theoretical peptides allowing "
+ "at most -t miscleavages. It should be in the same "
+ "order than -enzymes options (e.g. -t 1 3 2). Only "
+ "for sequential digestion (default: 0)")
parser.add_argument("-n", "--noninteractive", action='store_true',
help="Non-interactive mode. No standard output, only "
"error(s) (--quiet enable, overwrite -v). If output "
@@ -441,6 +471,22 @@ def main():
aa_mass, water_mass,
args.processes)
+ # We need to compute all theoretical peptides for at least one enzyme
+ if args.theoretical:
+ # More mis cleavage than enzyme
+ if len(args.theoretical) > len(args.enzymes):
+ core.handle_errors("Too much miscleavage values. Last values will "
+ "be ignored.")
+ # Not enough mis cleavage values, complete with 0
+ elif len(args.theoretical) < len(args.enzymes):
+ args.theoretical += [0]*(len(args.enzymes) - len(args.theoretical))
+ # Dict of enzymes/max mis cleavage
+ enzymes_to_use = {}
+ # Link enzyme to mc value
+ for i, j in enumerate(args.enzymes):
+ enzymes_to_use[enzyme.get_enz_name(ALL_ENZYMES, j)] = args.theoretical[i]
+ # Compute the results
+ digest.theoretical_peptides(results_digestion, enzymes_to_use)
# Output results
core.output_results(output_file, results_digestion, args.fmt, args.quiet,
args.verbose)
diff --git a/rpg/digest.py b/rpg/digest.py
index 0ea2e64..f6a0dff 100644
--- a/rpg/digest.py
+++ b/rpg/digest.py
@@ -550,3 +550,60 @@ def digest_from_input(input_data, input_type, enz, mode, aa_pka, aa_mass, water_
input_type, 0, "Input ")
# Return all peptides
return results_digestion
+
+def theoretical_peptides(results_digestion, mc_val):
+ """ Add in results_digestion the resulting peptides of mis cleaved
+ positions
+
+ :param results_digestion: result of digestions
+ :param mc_val: maxima number of mis cleavage per enzyme
+ :type results_digestion: list(list(:py:class:`ResultOneDigestion`))
+ :type mc_val: dict(enzyme_name: value)
+ """
+ # For each digested sequence
+ for a_seq in results_digestion:
+ # For each digestion results
+ for a_dig_res in a_seq:
+ # This result of digestion need to be undigested
+ if mc_val[a_dig_res.enzyme_name] != 0:
+ # Initial list of peptides (ordered by construction)
+ cur_peptides = list(a_dig_res.peptides)
+ # Id of the last peptide of this digestion
+ cur_id_pep = cur_peptides[-1].nb_peptide
+ # Current number of mis cleavage accepted
+ cur_mc_val = 1
+ # We still need to merge peptide
+ while cur_mc_val <= mc_val[a_dig_res.enzyme_name]:
+ # For each peptide
+ for i in range(len(cur_peptides) - cur_mc_val):
+ # Get the peptides to merge
+ some_pep = cur_peptides[i:i+cur_mc_val+1]
+ # Take the header of the first peptide
+ header = some_pep[0].header
+ # Take the enzyme name of the first peptide
+ enzyme_name = some_pep[0].enzyme_name
+ # Take the pka of the first peptide
+ aa_pka = some_pep[0].aa_pka
+ # Take the aa masses of the first peptide
+ aa_mass = some_pep[0].aa_mass
+ # Take the water mass of the first peptide
+ water_mass = some_pep[0].water_mass
+ # Next nb_pep
+ cur_id_pep += 1
+ nb_peptide = cur_id_pep
+ # Take the cleavage position of the last peptide
+ position = some_pep[-1].position
+ # Merge the sequences
+ seq = "".join(x.sequence for x in some_pep)
+ # New peptide
+ new_pep = sequence.Peptide(header,
+ seq,
+ enzyme_name,
+ aa_pka,
+ aa_mass,
+ water_mass,
+ nb_peptide,
+ position)
+ a_dig_res.peptides.append(new_pep)
+ # Increase number of mis cleavage
+ cur_mc_val += 1
diff --git a/rpg/enzyme.py b/rpg/enzyme.py
index cb34adc..4c496b9 100644
--- a/rpg/enzyme.py
+++ b/rpg/enzyme.py
@@ -93,6 +93,31 @@ class Enzyme:
core.handle_errors("'%s' can't be open in '%s' mode" %
(enz_file, "a"), 0, "File ")
+def get_enz_name(all_enzymes, name):
+ """ Get the proper name of an enzyme
+
+ :param all_enzymes: all already existing enzymes
+ :param name: name or id of the enzyme
+ :type all_enzymes: list(:py:class:`~rpg.enzyme.Enzyme`)
+ :type name: str
+
+ :return: The real name of an enzyme
+ :rtype: str
+ """
+ enz_name = None
+ # Get the name
+ for i in all_enzymes:
+ # Get the name of this enzyme
+ if (str(name).isdigit() and i.id_ == int(name)) or \
+ i.name.casefold() == str(name).casefold():
+ enz_name = i.name.strip()
+ break
+ # Enzyme not found
+ if not enz_name:
+ core.handle_errors(f"Not able to find enzyme {name}.", 0)
+ # Return the correct name of this enzyme
+ return enz_name
+
def check_enzyme_name(name_new_enz, all_name_enz):
"""Validate the name of a new enzyme.
@@ -105,7 +130,7 @@ def check_enzyme_name(name_new_enz, all_name_enz):
:rtype: bool
Enzyme name should not contains whitespace character (' ', \\\\t,
- \\\\n, \\\\r, \\\\f, \\\\v), be empty or be already used.
+ \\\\n, \\\\r, \\\\f, \\\\v), be empty, a digit or be already used.
"""
ret = True
@@ -114,6 +139,12 @@ def check_enzyme_name(name_new_enz, all_name_enz):
core.handle_errors("This name exist, please choose another name.", 2)
ret = False
+ # Does it contain only digit character?
+ if name_new_enz.isdigit():
+ core.handle_errors("Enzyme name can't be only digits, please choose"\
+ " another name.", 2)
+ ret = False
+
# Does it contain ' ' character?
res = re.search(" ", name_new_enz)
if res:
@@ -393,7 +424,7 @@ def delete_enzyme(all_enzymes, name):
:type all_enzymes: list(:py:class:`~rpg.enzyme.Enzyme`)
:type name: str
- .. warning:: Partially tested, remove bu ID can't be tested
+ .. warning:: Partially tested, remove by ID can't be tested
"""
user_content = ""
# Get the whole content of user file
@@ -401,17 +432,8 @@ def delete_enzyme(all_enzymes, name):
for line in user_file:
user_content += line
- # We have an id, not a name of enzyme
- if name.isdigit():
- # Get the name
- for i in all_enzymes:
- # Get the name of this enzyme
- if i.id_ == int(name):
- enz_name = i.name.strip()
- break
- else:
- # Use the given name
- enz_name = name.strip()
+ # Get the name of the enzyme
+ enz_name = get_enz_name(all_enzymes, name)
# Beginning of what to remove
beg_to_detect = f"# User-defined enzyme {re.escape(enz_name)}\n"
diff --git a/tests/test_digest.py b/tests/test_digest.py
index 5c42a08..edec331 100644
--- a/tests/test_digest.py
+++ b/tests/test_digest.py
@@ -554,3 +554,7 @@ def test_digest_part(tmpdir):
# We have a ValueError
assert pytest_wrapped_e.type == ValueError
assert str(pytest_wrapped_e.value) == "input file format not recognized (,)."
+
+def test_theoretical_peptides(capsys):
+ """Test function 'theoretical_peptides(results_digestion, mc_val)'"""
+ pass
\ No newline at end of file
diff --git a/tests/test_enzyme.py b/tests/test_enzyme.py
index a617aa7..2c8365f 100644
--- a/tests/test_enzyme.py
+++ b/tests/test_enzyme.py
@@ -162,8 +162,23 @@ def test_delete_enzyme(capsys):
for line in usr_file:
nb_line += 1
assert nb_line == 27
+ # Virtually add enzyme Pwet-42
+ tmp = list(AVAILABLE_ENZYMES)
+ ENZ = []
+
+ C_1 = rule.Rule(0, "C", True, 1) # Always cleaves after C, except...
+ C_1E1 = rule.Rule(1, "E", False, -1) # Never cleaves after C, followed by E, except...
+ C_1.rules.append(C_1E1)
+ ENZ.append(C_1)
+
+ D_1 = rule.Rule(0, "D", True, 1) # Always cleaves after D, except...
+ ENZ.append(D_1)
+
+ ENZYME = enzyme.Enzyme(44, "Pwet-42", ENZ, 0)
+ # Add it to available enzymes
+ tmp.append(ENZYME)
# Delete it
- enzyme.delete_enzyme(AVAILABLE_ENZYMES, "Pwet-42")
+ enzyme.delete_enzyme(tmp, "Pwet-42")
# Normal process
all_enz = AVAILABLE_ENZYMES
@@ -183,8 +198,20 @@ def test_delete_enzyme(capsys):
for line in usr_file:
nb_line += 1
assert nb_line == 22
+
+ # Virtually add enzyme Pwet
+ tmp = list(AVAILABLE_ENZYMES)
+ ENZ = []
+
+ R_1 = rule.Rule(0, "R", True, 1) # Always cleaves after R, except...
+ ENZ.append(R_1)
+
+ ENZYME = enzyme.Enzyme(44, "Pwet", ENZ, 0)
+ # Add it to available enzymes
+ tmp.append(ENZYME)
+
# Delete it
- enzyme.delete_enzyme(AVAILABLE_ENZYMES, "Pwet")
+ enzyme.delete_enzyme(tmp, "Pwet")
# We should be back at 11 lines
nb_line = 1
with open(user_file) as usr_file:
@@ -192,7 +219,7 @@ def test_delete_enzyme(capsys):
nb_line += 1
assert nb_line == 9
- # Wrong name
+ # Wrong name to delete
name = "Pwet"
rules = ["(R,)"]
# Number of line of user file before inserting an enzyme
@@ -209,14 +236,26 @@ def test_delete_enzyme(capsys):
for line in usr_file:
nb_line += 1
assert nb_line == 22
+
+ # Virtually add enzyme Pwet
+ tmp = list(AVAILABLE_ENZYMES)
+ ENZ = []
+
+ R_1 = rule.Rule(0, "R", True, 1) # Always cleaves after R, except...
+ ENZ.append(R_1)
+
+ ENZYME = enzyme.Enzyme(44, "Pwet", ENZ, 0)
+ # Add it to available enzymes
+ tmp.append(ENZYME)
+
# Delete it
with pytest.raises(SystemExit) as pytest_wrapped_e:
enzyme.delete_enzyme(AVAILABLE_ENZYMES, "Pwett")
_, err = capsys.readouterr()
- assert err == "Error: Not able to remove enzyme Pwett, please remove manually\n"
+ assert err == "Error: Not able to find enzyme Pwett.\n"
assert pytest_wrapped_e.type == SystemExit
assert pytest_wrapped_e.value.code == 1
- enzyme.delete_enzyme(AVAILABLE_ENZYMES, "Pwet")
+ enzyme.delete_enzyme(tmp, "Pwet")
# We should be back at 11 lines
nb_line = 1
with open(user_file) as usr_file:
@@ -241,11 +280,40 @@ def test_delete_enzyme(capsys):
for line in usr_file:
nb_line += 1
assert nb_line == 22
+ # Virtually add enzyme Pwet
+ tmp = list(AVAILABLE_ENZYMES)
+ ENZ = []
+
+ R_1 = rule.Rule(0, "R", True, 1) # Always cleaves after R, except...
+ ENZ.append(R_1)
+
+ ENZYME = enzyme.Enzyme(44, "Pwe.[t", ENZ, 0)
+ # Add it to available enzymes
+ tmp.append(ENZYME)
# Delete it
- enzyme.delete_enzyme(AVAILABLE_ENZYMES, "Pwe.[t")
+ enzyme.delete_enzyme(tmp, "Pwe.[t")
# We should be back at 11 lines
nb_line = 1
with open(user_file) as usr_file:
for line in usr_file:
nb_line += 1
assert nb_line == 9
+
+def test_get_enz_name(capsys):
+ """Test function 'get_enz_name()'."""
+ # Enzyme does not exist
+ with pytest.raises(SystemExit) as pytest_wrapped_e:
+ enzyme.get_enz_name(AVAILABLE_ENZYMES, "Pwett")
+ _, err = capsys.readouterr()
+ assert err == "Error: Not able to find enzyme Pwett.\n"
+ assert pytest_wrapped_e.type == SystemExit
+ assert pytest_wrapped_e.value.code == 1
+
+ # Normal behavior
+ assert enzyme.get_enz_name(AVAILABLE_ENZYMES, 42) == "Trypsin"
+
+ # Normal behavior
+ assert enzyme.get_enz_name(AVAILABLE_ENZYMES, "42") == "Trypsin"
+
+ # Normal behavior
+ assert enzyme.get_enz_name(AVAILABLE_ENZYMES, "trypsin") == "Trypsin"
\ No newline at end of file
diff --git a/tests/test_functional.py b/tests/test_functional.py
index 8cda12d..aaa9e53 100644
--- a/tests/test_functional.py
+++ b/tests/test_functional.py
@@ -7,6 +7,8 @@ from pathlib import Path
from io import StringIO
from .context import rpg
from rpg import RapidPeptidesGenerator
+from rpg import enzyme
+from rpg import rule
@pytest.fixture
def truth():
@@ -550,6 +552,58 @@ def res_dig_1_42():
">Input_8_Trypsin_47_3_407.46678_3.74\n"\
"EFL\n"
+@pytest.fixture
+def res_dig_1_42_2():
+ """ Result for digestion with 1 and 42 and IPC2 """
+ return ">Input_0_Trypsin_2_2_289.29138_5.98\n"\
+ "DR\n"\
+ ">Input_1_Trypsin_10_8_935.00128_4.29\n"\
+ "EALDSSWK\n"\
+ ">Input_2_Trypsin_11_1_146.18938_8.06\n"\
+ "K\n"\
+ ">Input_3_Trypsin_13_2_287.36218_9.71\n"\
+ "LR\n"\
+ ">Input_4_Trypsin_19_6_503.51548_9.71\n"\
+ "SGAGGR\n"\
+ ">Input_5_Trypsin_20_1_146.18938_8.06\n"\
+ "K\n"\
+ ">Input_6_Trypsin_25_5_529.59668_9.71\n"\
+ "NAGIR\n"\
+ ">Input_7_Trypsin_44_19_2283.62998_4.3\n"\
+ "LVLWMLDFDAHQPDSVLQR\n"\
+ ">Input_8_Trypsin_47_3_407.46678_3.74\n"\
+ "EFL\n"\
+ ">Input_9_Trypsin_10_10_1206.27738_4.49\n"\
+ "DREALDSSWK\n"\
+ ">Input_10_Trypsin_11_9_1063.17538_6.12\n"\
+ "EALDSSWKK\n"\
+ ">Input_11_Trypsin_13_3_415.53628_9.93\n"\
+ "KLR\n"\
+ ">Input_12_Trypsin_19_8_772.86238_11.49\n"\
+ "LRSGAGGR\n"\
+ ">Input_13_Trypsin_20_7_631.68958_9.93\n"\
+ "SGAGGRK\n"\
+ ">Input_14_Trypsin_25_6_657.77078_9.93\n"\
+ "KNAGIR\n"\
+ ">Input_15_Trypsin_44_24_2795.21138_5.46\n"\
+ "NAGIRLVLWMLDFDAHQPDSVLQR\n"\
+ ">Input_16_Trypsin_47_22_2673.08148_4.12\n"\
+ "LVLWMLDFDAHQPDSVLQREFL\n"\
+ ">Input_17_Trypsin_11_11_1334.45148_6.16\n"\
+ "DREALDSSWKK\n"\
+ ">Input_18_Trypsin_13_11_1332.52228_7.79\n"\
+ "EALDSSWKKLR\n"\
+ ">Input_19_Trypsin_19_9_901.03648_11.49\n"\
+ "KLRSGAGGR\n"\
+ ">Input_20_Trypsin_20_9_901.03648_11.49\n"\
+ "LRSGAGGRK\n"\
+ ">Input_21_Trypsin_25_12_1143.27098_11.49\n"\
+ "SGAGGRKNAGIR\n"\
+ ">Input_22_Trypsin_44_25_2923.38548_7.08\n"\
+ "KNAGIRLVLWMLDFDAHQPDSVLQR\n"\
+ ">Input_23_Trypsin_47_27_3184.66288_4.61\n"\
+ "NAGIRLVLWMLDFDAHQPDSVLQREFL\n"
+
@pytest.fixture
def res_dig_1_42_ipc():
""" Result for digestion with 1 and 42 """
@@ -1106,20 +1160,51 @@ def test_na_option(capsys):
nb_line += 1
assert nb_line == 24
- # Test -b behavior
- with pytest.raises(SystemExit) as pytest_wrapped_e:
- with unittest.mock.patch("sys.argv", ["func_test",
- "-b", "Pwet"]):
- RapidPeptidesGenerator.main()
- assert pytest_wrapped_e.value.code == 0
- # Output
- captured = capsys.readouterr()
- # Check result
- user_file = str(Path.home()) + "/rpg_user.py"
+ # Virtually add enzyme Pwet
+ tmp = []
+ ENZ = []
- # Number of line of user file after inserting enzyme in previous test
+ R_1 = rule.Rule(0, "R", True, 1) # Always cleaves after R, except...
+ ENZ.append(R_1)
+
+ ENZYME = enzyme.Enzyme(44, "Pwet", ENZ, 0)
+ # Add it to available enzymes
+ tmp.append(ENZYME)
+ # Delete the enzyme
+ enzyme.delete_enzyme(tmp, "Pwet")
+ # We should be back at 11 lines
nb_line = 1
with open(user_file) as usr_file:
for line in usr_file:
nb_line += 1
assert nb_line == 9
+
+def test_theoretical(capsys, monkeypatch, list_enz, res_dig_1_42_2):
+ """ Test correct behavior """
+ with unittest.mock.patch("sys.argv", ["func_test",
+ "-s", "DREALDSSWKKLRSgagGRKNAGI"\
+ "RLVLWMLDFDAHQPDSVLQREFL",
+ "-e", "42",
+ "-t", "1", "2", "3"]):
+ RapidPeptidesGenerator.main()
+ captured = capsys.readouterr()
+ assert "Too much miscleavage values. Last values will be ignored.\n" in captured.err
+
+
+ with unittest.mock.patch("sys.argv", ["func_test",
+ "-s", "DREALDSSWKKLRSgagGRKNAGI"\
+ "RLVLWMLDFDAHQPDSVLQREFL",
+ "-e", "42",
+ "-t", "2"]):
+ RapidPeptidesGenerator.main()
+ captured = capsys.readouterr()
+ assert res_dig_1_42_2 in captured.out
+
+ with unittest.mock.patch("sys.argv", ["func_test",
+ "-s", "DREALDSSWKKLRSgagGRKNAGI"\
+ "RLVLWMLDFDAHQPDSVLQREFL",
+ "-e", "42", "2",
+ "-t", "2"]):
+ RapidPeptidesGenerator.main()
+ captured = capsys.readouterr()
+ assert res_dig_1_42_2 in captured.out
--
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