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Commit 18551f60 authored by Nicolas MAILLET's avatar Nicolas MAILLET
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Add IPC2 to RPG and make it the default one

parent dce7a910
Pipeline #57012 passed with stages
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rpg/RapidPeptidesGenerator.py
View file @ 18551f60
......@@ -272,9 +272,9 @@ def main():
"error(s) (--quiet enable, overwrite -v). If output "
"filename already exists, output file will be "
"overwritten.")
parser.add_argument("-p", "--pka", metavar="", choices=['ipc', 'stryer'],
default="ipc", help="Define pKa values. Either 'ipc' "
"or 'stryer' (default: ipc)")
parser.add_argument("-p", "--pka", metavar="", choices=['ipc2', 'stryer', 'ipc'],
default="ipc2", help="Define pKa values. Either 'ipc2' "
"'stryer' or 'ipc' (deprecated) (default: ipc2)")
group_output = parser.add_mutually_exclusive_group()
group_output.add_argument("-o", "--outputfile", type=str, metavar="",
default="", help="Optional result file "
......@@ -306,9 +306,11 @@ def main():
args.miscleavage = [] # No miscleavage on concurrent, infinite time
# --pka option
aa_pka = core.AA_PKA_IPC
aa_pka = core.AA_PKA_IPC_2
if args.pka == "stryer":
aa_pka = core.AA_PKA_S
elif args.pka == "ipc":
aa_pka = core.AA_PKA_IPC
# --list option
if args.list:
......
rpg/core.py
View file @ 18551f60
......@@ -86,6 +86,17 @@ AA_PKA_IPC = {"Nterm" : 9.564,
"Y" : 10.071,
"Cterm" : 2.383}
"""pKa of important amino acid to compute pI (from IPC_peptide. See http://isoelectric.org/theory.html for details)."""
# IPC_peptide2
AA_PKA_IPC_2 = {"Nterm" : 7.947,
"C" : 9.454,
"D" : 3.969,
"E" : 4.507,
"H" : 6.439,
"K" : 8.165,
"R" : 11.493,
"Y" : 9.153,
"Cterm" : 2.977}
"""pKa of important amino acid to compute pI (from IPC_peptide2. See http://www.ipc2-isoelectric-point.org/ for details)."""
def handle_errors(message="", err=1, error_type=""):
"""Custom handling of errors and warnings.
......
rpg/sequence.py
View file @ 18551f60
......@@ -68,9 +68,11 @@ class Peptide:
# self representation for print
def __repr__(self):
pka = "IPC"
pka = "IPC2"
if self.aa_pka == core.AA_PKA_S:
pka = "Stryer"
elif self.aa_pka == core.AA_PKA_IPC:
pka = "IPC"
return "Original header: " + self.header + "\nNo. peptide: " + \
str(self.nb_peptide) + "\nEnzyme: " + self.enzyme_name + \
"\nCleav. pos: " + str(self.position) + "\nPep. size: " + \
......
tests/test_functional.py
View file @ 18551f60
......@@ -9,6 +9,220 @@ from rpg import RapidPeptidesGenerator
@pytest.fixture
def truth():
""" Solution """
return [">A0A2C9KB11/1065-1162_0_Trypsin_2_2_289.29138_5.98\n",
"DR\n",
">A0A2C9KB11/1065-1162_1_Trypsin_10_8_935.00128_4.29\n",
"EALDSSWK\n",
">A0A2C9KB11/1065-1162_2_Trypsin_11_1_146.18938_8.06\n",
"K\n",
">A0A2C9KB11/1065-1162_3_Trypsin_13_2_287.36218_9.71\n",
"LR\n",
">A0A2C9KB11/1065-1162_4_Trypsin_19_6_503.51548_9.71\n",
"SGAGGR\n",
">A0A2C9KB11/1065-1162_5_Trypsin_20_1_146.18938_8.06\n",
"K\n",
">A0A2C9KB11/1065-1162_6_Trypsin_25_5_529.59668_9.71\n",
"NAGIR\n",
">A0A2C9KB11/1065-1162_7_Trypsin_38_13_1623.99478_7.2\n",
"LVLWMLDHVPNMR\n",
">A0A2C9KB11/1065-1162_8_Trypsin_42_4_535.60048_8.06\n",
"NQFK\n",
">A0A2C9KB11/1065-1162_9_Trypsin_43_1_146.18938_8.06\n",
"K\n",
">A0A2C9KB11/1065-1162_10_Trypsin_54_11_1297.43618_7.2\n",
"FAHQPDSVLQR\n",
">A0A2C9KB11/1065-1162_11_Trypsin_64_10_1189.29028_3.89\n",
"DPEFLAQVDR\n",
">A0A2C9KB11/1065-1162_12_Trypsin_88_24_2545.84688_3.63\n",
"ILGGVESMINNVDDPVALEAAFDR\n",
">A0A2C9KB11/1065-1162_13_Trypsin_97_9_958.09728_5.22\n",
"LADAHLSMT\n",
">A0A2C9KB11/1221-1332_0_Trypsin_2_2_303.31828_6.23\n",
"ER\n",
">A0A2C9KB11/1221-1332_1_Trypsin_3_1_146.18938_8.06\n",
"K\n",
">A0A2C9KB11/1221-1332_2_Trypsin_6_3_330.42758_8.06\n",
"ALK\n",
">A0A2C9KB11/1221-1332_3_Trypsin_13_7_821.88518_5.87\n",
"SSWDSLK\n",
">A0A2C9KB11/1221-1332_4_Trypsin_38_25_2643.03068_6.23\n",
"SAAGGSQEAGVNLVLWMLQNVPNMR\n",
">A0A2C9KB11/1221-1332_5_Trypsin_40_2_289.29138_5.98\n",
"DR\n",
">A0A2C9KB11/1221-1332_6_Trypsin_53_13_1463.56938_5.37\n",
"FTFNAHQGDDALK\n",
">A0A2C9KB11/1221-1332_7_Trypsin_60_7_792.88708_4.29\n",
"ADAEFIK\n",
">A0A2C9KB11/1221-1332_8_Trypsin_64_4_529.59678_9.71\n",
"QVQR\n",
">A0A2C9KB11/1221-1332_9_Trypsin_81_17_1804.98958_3.89\n",
"ITGGLESMIDNLDNQGK\n",
">A0A2C9KB11/1221-1332_10_Trypsin_88_7_785.89848_5.98\n",
"LQAAIDR\n",
">A0A2C9KB11/1221-1332_11_Trypsin_110_22_2524.91728_5.5\n",
"LVDAHLHMTPSVGLEYFEPLQK\n",
">A0A2C9KB11/1221-1332_12_Trypsin_111_1_132.11908_5.46\n",
"N\n",
">A0A2C9KB11/1378-1486_0_Trypsin_2_2_289.29138_5.98\n",
"DR\n",
">A0A2C9KB11/1378-1486_1_Trypsin_3_1_146.18938_8.06\n",
"K\n",
">A0A2C9KB11/1378-1486_2_Trypsin_10_7_912.00988_6.12\n",
"YIESSWK\n",
">A0A2C9KB11/1378-1486_3_Trypsin_11_1_146.18938_8.06\n",
"K\n",
">A0A2C9KB11/1378-1486_4_Trypsin_21_10_947.99758_4.29\n",
"LTDAAGGSEK\n",
">A0A2C9KB11/1378-1486_5_Trypsin_38_17_1994.29828_5.98\n",
"AGTNFVFWLLDNVPNMR\n",
">A0A2C9KB11/1378-1486_6_Trypsin_40_2_289.29138_5.98\n",
"DR\n",
">A0A2C9KB11/1378-1486_7_Trypsin_59_19_2255.34168_4.12\n",
"FTFNAHQSDAALQEDEEFR\n",
">A0A2C9KB11/1378-1486_8_Trypsin_63_4_487.55648_8.06\n",
"NQVK\n",
">A0A2C9KB11/1378-1486_9_Trypsin_108_45_4677.21938_4.05\n",
"AITGGIESFVNNVNNPAALQSSIETLVDAHLNMQPSIGLSYFGSV\n",
">A0A2C9KB11/1535-1643_0_Trypsin_2_2_289.29138_5.98\n",
"DR\n",
">A0A2C9KB11/1535-1643_1_Trypsin_3_1_174.20278_9.71\n",
"R\n",
">A0A2C9KB11/1535-1643_2_Trypsin_10_7_775.90298_8.06\n",
"AVVSSWK\n",
">A0A2C9KB11/1535-1643_3_Trypsin_11_1_146.18938_8.06\n",
"K\n",
">A0A2C9KB11/1535-1643_4_Trypsin_17_6_603.67618_9.71\n",
"LTASGR\n",
">A0A2C9KB11/1535-1643_5_Trypsin_36_19_2281.67528_5.98\n",
"QSFGIDLVLWMFNNVPNMR\n",
">A0A2C9KB11/1535-1643_6_Trypsin_44_8_985.06128_4.29\n",
"EQFTFDAK\n",
">A0A2C9KB11/1535-1643_7_Trypsin_51_7_803.82708_4.04\n",
"QSDADLR\n",
">A0A2C9KB11/1535-1643_8_Trypsin_52_1_174.20278_9.71\n",
"R\n",
">A0A2C9KB11/1535-1643_9_Trypsin_58_6_732.83448_5.87\n",
"DPNFLK\n",
">A0A2C9KB11/1535-1643_10_Trypsin_79_21_2158.36788_3.75\n",
"QVNSIVNGLGDMVDSVNDPGK\n",
">A0A2C9KB11/1535-1643_11_Trypsin_86_7_842.95038_6.23\n",
"LQANLER\n",
">A0A2C9KB11/1535-1643_12_Trypsin_108_22_2521.94168_5.57\n",
"LSEIHLHFVPSVGPEFFVPLEK\n",
">A0A2C9K1A5/128-239_0_Trypsin_3_3_374.43738_5.87\n",
"DIK\n",
">A0A2C9K1A5/128-239_1_Trypsin_11_8_919.98958_5.87\n",
"ALDSSWNK\n",
">A0A2C9K1A5/128-239_2_Trypsin_19_8_759.81728_5.98\n",
"LTAGADGR\n",
">A0A2C9K1A5/128-239_3_Trypsin_37_18_2120.51518_9.71\n",
"TTFGNNLVLWMLNVPNMR\n",
">A0A2C9K1A5/128-239_4_Trypsin_39_2_303.31828_6.23\n",
"ER\n",
">A0A2C9K1A5/128-239_5_Trypsin_42_3_392.49858_8.06\n",
"FVK\n",
">A0A2C9K1A5/128-239_6_Trypsin_53_11_1259.34088_5.53\n",
"FNAHQSDEALK\n",
">A0A2C9K1A5/128-239_7_Trypsin_60_7_835.91208_4.29\n",
"NDAEFIK\n",
">A0A2C9K1A5/128-239_8_Trypsin_63_3_373.45268_8.06\n",
"QVK\n",
">A0A2C9K1A5/128-239_9_Trypsin_111_48_5318.17868_6.16\n",
"LIVGGLQTLIINLNNPGQLQASIEHLADVHLHMKPSIGLEYFKPLQEN\n",
">A0A2C9K1A5/285-395_0_Trypsin_2_2_261.27798_5.87\n",
"DK\n",
">A0A2C9K1A5/285-395_1_Trypsin_11_9_1034.13688_6.23\n",
"VALESSWSR\n",
">A0A2C9K1A5/285-395_2_Trypsin_19_8_758.87288_8.06\n",
"LTAGVNGK\n",
">A0A2C9K1A5/285-395_3_Trypsin_20_1_174.20278_9.71\n",
"R\n",
">A0A2C9K1A5/285-395_4_Trypsin_25_5_515.56988_9.71\n",
"NAGVR\n",
">A0A2C9K1A5/285-395_5_Trypsin_37_12_1520.87088_5.98\n",
"LVLWMFNVPDMR\n",
">A0A2C9K1A5/285-395_6_Trypsin_39_2_303.31828_6.23\n",
"ER\n",
">A0A2C9K1A5/285-395_7_Trypsin_42_3_422.48448_9.71\n",
"FTR\n",
">A0A2C9K1A5/285-395_8_Trypsin_46_4_478.54858_8.06\n",
"FNAK\n",
">A0A2C9K1A5/285-395_9_Trypsin_53_7_789.84058_4.29\n",
"QSDEALK\n",
">A0A2C9K1A5/285-395_10_Trypsin_60_7_822.91338_4.29\n",
"TDAEFLK\n",
">A0A2C9K1A5/285-395_11_Trypsin_85_25_2798.14518_3.68\n",
"QVDVIIGGFETLINNLNDPTLLQDR\n",
">A0A2C9K1A5/285-395_12_Trypsin_96_11_1225.36408_4.66\n",
"LESLADAHLEK\n",
">A0A2C9K1A5/285-395_13_Trypsin_110_14_1504.79238_8.32\n",
"KPAIGVSYFGPLQK\n",
">A0A2C9K1A5/588-698_0_Trypsin_2_2_261.27798_5.87\n",
"DK\n",
">A0A2C9K1A5/588-698_1_Trypsin_3_1_146.18938_8.06\n",
"K\n",
">A0A2C9K1A5/588-698_2_Trypsin_25_22_2285.50118_8.06\n",
"ALQSSWNTLVNQAGGQQNAGIK\n",
">A0A2C9K1A5/588-698_3_Trypsin_37_12_1519.88608_9.71\n",
"LVLWMFNVPNMR\n",
">A0A2C9K1A5/588-698_4_Trypsin_39_2_289.29138_5.98\n",
"DR\n",
">A0A2C9K1A5/588-698_5_Trypsin_42_3_380.44418_8.06\n",
"FSK\n",
">A0A2C9K1A5/588-698_6_Trypsin_53_11_1204.26148_5.37\n",
"FNAHSSDDALK\n",
">A0A2C9K1A5/588-698_7_Trypsin_60_7_792.88708_4.29\n",
"ADAEFLK\n",
">A0A2C9K1A5/588-698_8_Trypsin_81_21_2198.41478_3.68\n",
"QVNVIVGGLESLVNNVDDADK\n",
">A0A2C9K1A5/588-698_9_Trypsin_88_7_771.87168_6.23\n",
"LQAGVER\n",
">A0A2C9K1A5/588-698_10_Trypsin_110_22_2438.78338_5.38\n",
"LVDAHLHMSPSVGLEYFGPLQQ\n",
">A0A2C9K1A5/745-855_0_Trypsin_2_2_289.29138_5.98\n",
"DR\n",
">A0A2C9K1A5/745-855_1_Trypsin_3_1_146.18938_8.06\n",
"K\n",
">A0A2C9K1A5/745-855_2_Trypsin_7_4_515.61028_6.23\n",
"VLER\n",
">A0A2C9K1A5/745-855_3_Trypsin_19_12_1257.41158_8.06\n",
"TWNQLISGPGGK\n",
">A0A2C9K1A5/745-855_4_Trypsin_21_2_275.30488_6.13\n",
"EK\n",
">A0A2C9K1A5/745-855_5_Trypsin_25_4_387.47948_8.06\n",
"AGIK\n",
">A0A2C9K1A5/745-855_6_Trypsin_38_13_1649.00158_6.23\n",
"LVLWMFENVPNMR\n",
">A0A2C9K1A5/745-855_7_Trypsin_43_5_623.66348_5.87\n",
"DQFSK\n",
">A0A2C9K1A5/745-855_8_Trypsin_48_5_616.67448_7.08\n",
"FDAHK\n",
">A0A2C9K1A5/745-855_9_Trypsin_60_12_1349.50358_4.67\n",
"SDEALSKPEFVK\n",
">A0A2C9K1A5/745-855_10_Trypsin_96_36_3961.35988_4.38\n",
"QVNNIFGGLESILNNLNKPGQLQSALENLADDHLDR\n",
">A0A2C9K1A5/745-855_11_Trypsin_99_3_399.49358_9.93\n",
"KPR\n",
">A0A2C9K1A5/745-855_12_Trypsin_110_11_1248.48748_6.13\n",
"IGLEFFGPLQK\n",
">A0A2C9K1A5/935-1004_0_Trypsin_10_10_1288.50498_7.2\n",
"QMFEHVPNMR\n",
">A0A2C9K1A5/935-1004_1_Trypsin_15_5_651.71728_6.13\n",
"EQFTK\n",
">A0A2C9K1A5/935-1004_2_Trypsin_26_11_1211.34268_7.08\n",
"FDAHQPNAALK\n",
">A0A2C9K1A5/935-1004_3_Trypsin_37_11_1258.39948_6.23\n",
"QNPEFLAQVGR\n",
">A0A2C9K1A5/935-1004_4_Trypsin_55_18_1881.15618_3.89\n",
"ILGGIESLLNNDDPVALK\n",
">A0A2C9K1A5/935-1004_5_Trypsin_60_5_544.60838_5.98\n",
"AAIDR\n",
">A0A2C9K1A5/935-1004_6_Trypsin_69_9_944.07038_5.22\n",
"LADAHLSMS\n"]
@pytest.fixture
def truth_ipc():
""" Solution """
return [">A0A2C9KB11/1065-1162_0_Trypsin_2_2_289.29138_6.73\n",
"DR\n",
......@@ -302,6 +516,40 @@ def list_enz():
@pytest.fixture
def res_dig_1_42():
""" Result for digestion with 1 and 42 and IPC2 """
return ">Input_0_Arg-C_2_2_289.29138_5.98\n"\
"DR\n"\
">Input_1_Arg-C_13_11_1332.52228_7.79\n"\
"EALDSSWKKLR\n"\
">Input_2_Arg-C_19_6_503.51548_9.71\n"\
"SGAGGR\n"\
">Input_3_Arg-C_25_6_657.77078_9.93\n"\
"KNAGIR\n"\
">Input_4_Arg-C_44_19_2283.62998_4.3\n"\
"LVLWMLDFDAHQPDSVLQR\n"\
">Input_5_Arg-C_47_3_407.46678_3.74\n"\
"EFL\n"\
">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"
@pytest.fixture
def res_dig_1_42_ipc():
""" Result for digestion with 1 and 42 """
return ">Input_0_Arg-C_2_2_289.29138_6.73\n"\
"DR\n"\
......@@ -424,6 +672,17 @@ def test_s_option(capsys, res_dig_1_42):
captured = capsys.readouterr()
assert res_dig_1_42 in captured.out
def test_s_option_ipc(capsys, res_dig_1_42_ipc):
""" Test -s behavior """
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "DREALDSSWKKLRSgagGRKNAGI"\
"RLVLWMLDFDAHQPDSVLQREFL",
"-e", "1", "42", "-p", "ipc"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert res_dig_1_42_ipc in captured.out
def test_d_option(capsys):
""" Test -d behavior """
# sequential
......@@ -433,6 +692,40 @@ def test_d_option(capsys):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert ">Input_0_Lys-C_2_2_243.30608_8.06\nPK\n"\
">Input_1_Lys-C_4_2_243.30608_8.06\nPK\n"\
">Input_2_Lys-C_6_2_243.30608_8.06\nPK\n"\
">Input_3_Lys-C_8_2_243.30608_8.06\nPK\n"\
">Input_0_Lys-N_1_1_115.13198_5.46\nP\n"\
">Input_1_Lys-N_3_2_243.30608_8.06\nKP\n"\
">Input_2_Lys-N_5_2_243.30608_8.06\nKP\n"\
">Input_3_Lys-N_7_2_243.30608_8.06\nKP\n"\
">Input_4_Lys-N_8_1_146.18938_8.06\nK\n" in captured.out
# concurrent
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK",
"-e", "28", "29", "-d", "c"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert ">Input_0_Lys-C-Lys-N_1_1_115.13198_5.46\nP\n"\
">Input_1_Lys-C-Lys-N_2_1_146.18938_8.06\nK\n"\
">Input_2_Lys-C-Lys-N_3_1_115.13198_5.46\nP\n"\
">Input_3_Lys-C-Lys-N_4_1_146.18938_8.06\nK\n"\
">Input_4_Lys-C-Lys-N_5_1_115.13198_5.46\nP\n"\
">Input_5_Lys-C-Lys-N_6_1_146.18938_8.06\nK\n"\
">Input_6_Lys-C-Lys-N_7_1_115.13198_5.46\nP\n"\
">Input_7_Lys-C-Lys-N_8_1_146.18938_8.06\nK\n" in captured.out
def test_d_option_ipc(capsys):
""" Test -d behavior """
# sequential
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK", "-p", "ipc",
"-e", "28", "29", "-d", "s"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert "Input_0_Lys-C_2_2_243.30608_10.04\nPK\n"\
">Input_1_Lys-C_4_2_243.30608_10.04\nPK\n"\
">Input_2_Lys-C_6_2_243.30608_10.04\nPK\n"\
......@@ -444,7 +737,7 @@ def test_d_option(capsys):
">Input_4_Lys-N_8_1_146.18938_10.04\nK\n" in captured.out
# concurrent
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK",
"-s", "PKPKPKPK", "-p", "ipc",
"-e", "28", "29", "-d", "c"]):
RapidPeptidesGenerator.main()
# Output
......@@ -463,19 +756,19 @@ def test_p_option(capsys):
# default
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK",
"-e", "28", "29", "-p", "ipc"]):
"-e", "28", "29", "-p", "ipc2"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert "Input_0_Lys-C_2_2_243.30608_10.04\nPK\n"\
">Input_1_Lys-C_4_2_243.30608_10.04\nPK\n"\
">Input_2_Lys-C_6_2_243.30608_10.04\nPK\n"\
">Input_3_Lys-C_8_2_243.30608_10.04\nPK\n"\
">Input_0_Lys-N_1_1_115.13198_5.97\nP\n"\
">Input_1_Lys-N_3_2_243.30608_10.04\nKP\n"\
">Input_2_Lys-N_5_2_243.30608_10.04\nKP\n"\
">Input_3_Lys-N_7_2_243.30608_10.04\nKP\n"\
">Input_4_Lys-N_8_1_146.18938_10.04\nK\n" in captured.out
assert ">Input_0_Lys-C_2_2_243.30608_8.06\nPK\n"\
">Input_1_Lys-C_4_2_243.30608_8.06\nPK\n"\
">Input_2_Lys-C_6_2_243.30608_8.06\nPK\n"\
">Input_3_Lys-C_8_2_243.30608_8.06\nPK\n"\
">Input_0_Lys-N_1_1_115.13198_5.46\nP\n"\
">Input_1_Lys-N_3_2_243.30608_8.06\nKP\n"\
">Input_2_Lys-N_5_2_243.30608_8.06\nKP\n"\
">Input_3_Lys-N_7_2_243.30608_8.06\nKP\n"\
">Input_4_Lys-N_8_1_146.18938_8.06\nK\n" in captured.out
# stryer
with unittest.mock.patch("sys.argv", ["func_test",
......@@ -494,6 +787,23 @@ def test_p_option(capsys):
">Input_3_Lys-N_7_2_243.30608_9.4\nKP\n"\
">Input_4_Lys-N_8_1_146.18938_9.4\nK\n" in captured.out
# ipc
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK",
"-e", "28", "29", "-p", "ipc"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert ">Input_0_Lys-C_2_2_243.30608_10.04\nPK\n"\
">Input_1_Lys-C_4_2_243.30608_10.04\nPK\n"\
">Input_2_Lys-C_6_2_243.30608_10.04\nPK\n"\
">Input_3_Lys-C_8_2_243.30608_10.04\nPK\n"\
">Input_0_Lys-N_1_1_115.13198_5.97\nP\n"\
">Input_1_Lys-N_3_2_243.30608_10.04\nKP\n"\
">Input_2_Lys-N_5_2_243.30608_10.04\nKP\n"\
">Input_3_Lys-N_7_2_243.30608_10.04\nKP\n"\
">Input_4_Lys-N_8_1_146.18938_10.04\nK\n" in captured.out
def test_f_option(capsys):
""" Test -f behavior """
# default
......@@ -503,6 +813,63 @@ def test_f_option(capsys):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert ">Input_0_Lys-C_2_2_243.30608_8.06\nPK\n"\
">Input_1_Lys-C_4_2_243.30608_8.06\nPK\n"\
">Input_2_Lys-C_6_2_243.30608_8.06\nPK\n"\
">Input_3_Lys-C_8_2_243.30608_8.06\nPK\n"\
">Input_0_Lys-N_1_1_115.13198_5.46\nP\n"\
">Input_1_Lys-N_3_2_243.30608_8.06\nKP\n"\
">Input_2_Lys-N_5_2_243.30608_8.06\nKP\n"\
">Input_3_Lys-N_7_2_243.30608_8.06\nKP\n"\
">Input_4_Lys-N_8_1_146.18938_8.06\nK\n" in captured.out
# csv
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK",
"-e", "28", "29", "-f", "csv"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert "Original_header,No_peptide,Enzyme,Cleaving_pos,Peptide_size,"\
"Peptide_mass,pI,Sequence\n"\
"Input,0,Lys-C,2,2,243.30608,8.06,PK\n"\
"Input,1,Lys-C,4,2,243.30608,8.06,PK\n"\
"Input,2,Lys-C,6,2,243.30608,8.06,PK\n"\
"Input,3,Lys-C,8,2,243.30608,8.06,PK\n"\
"Input,0,Lys-N,1,1,115.13198,5.46,P\n"\
"Input,1,Lys-N,3,2,243.30608,8.06,KP\n"\
"Input,2,Lys-N,5,2,243.30608,8.06,KP\n"\
"Input,3,Lys-N,7,2,243.30608,8.06,KP\n"\
"Input,4,Lys-N,8,1,146.18938,8.06,K\n" in captured.out
# tsv
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK",
"-e", "28", "29", "-f", "tsv"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert "Original_header\tNo_peptide\tEnzyme\tCleaving_pos\tPeptide_size\t"\
"Peptide_mass\tpI\tSequence\n"\
"Input\t0\tLys-C\t2\t2\t243.30608\t8.06\tPK\n"\
"Input\t1\tLys-C\t4\t2\t243.30608\t8.06\tPK\n"\
"Input\t2\tLys-C\t6\t2\t243.30608\t8.06\tPK\n"\
"Input\t3\tLys-C\t8\t2\t243.30608\t8.06\tPK\n"\
"Input\t0\tLys-N\t1\t1\t115.13198\t5.46\tP\n"\
"Input\t1\tLys-N\t3\t2\t243.30608\t8.06\tKP\n"\
"Input\t2\tLys-N\t5\t2\t243.30608\t8.06\tKP\n"\
"Input\t3\tLys-N\t7\t2\t243.30608\t8.06\tKP\n"\
"Input\t4\tLys-N\t8\t1\t146.18938\t8.06\tK\n" in captured.out
def test_f_option_ipc(capsys):
""" Test -f behavior """
# default
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK", "-p", "ipc",
"-e", "28", "29", "-f", "fasta"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert "Input_0_Lys-C_2_2_243.30608_10.04\nPK\n"\
">Input_1_Lys-C_4_2_243.30608_10.04\nPK\n"\
">Input_2_Lys-C_6_2_243.30608_10.04\nPK\n"\
......@@ -515,7 +882,7 @@ def test_f_option(capsys):
# csv
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK",
"-s", "PKPKPKPK", "-p", "ipc",
"-e", "28", "29", "-f", "csv"]):
RapidPeptidesGenerator.main()
# Output
......@@ -534,7 +901,7 @@ def test_f_option(capsys):
# tsv
with unittest.mock.patch("sys.argv", ["func_test",
"-s", "PKPKPKPK",
"-s", "PKPKPKPK", "-p", "ipc",
"-e", "28", "29", "-f", "tsv"]):
RapidPeptidesGenerator.main()
# Output
......@@ -564,6 +931,19 @@ def test_i_option(capsys, truth, file_a):
for i in truth:
assert i in captured.out
def test_i_option_ipc(capsys, truth_ipc, file_a):
""" Test the functional behavior of FRAG of i option """
# Test -i behavior with fasta file
with unittest.mock.patch("sys.argv", ["func_test",
"-i", str(file_a),
"-e", "42", "-p", "ipc"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
# Check result
for i in truth_ipc:
assert i in captured.out
def test_i_option_parallel(capsys, truth, file_a):
""" Test the functional behavior of FRAG of i option """
# Test -i behavior with fasta file
......@@ -578,6 +958,20 @@ def test_i_option_parallel(capsys, truth, file_a):
for i in truth:
assert i in captured.out
def test_i_option_parallel_ipc(capsys, truth_ipc, file_a):
""" Test the functional behavior of FRAG of i option """
# Test -i behavior with fasta file
with unittest.mock.patch("sys.argv", ["func_test",
"-i", str(file_a),
"-e", "42",
"-c", "8", "-p", "ipc"]):
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
# Check result
for i in truth_ipc:
assert i in captured.out
def test_o_option(tmpdir, truth, file_a):
""" Test the functional behavior of FRAG of o (and q) option """
# Output folder
......@@ -599,6 +993,27 @@ def test_o_option(tmpdir, truth, file_a):
assert line in truth
assert nb_line == len(truth)
def test_o_option_ipc(tmpdir, truth_ipc, file_a):
""" Test the functional behavior of FRAG of o (and q) option """
# Output folder
output_folder = tmpdir.mkdir("res_functional_tests")
# Test -o behavior with fasta file
with unittest.mock.patch("sys.argv", ["func_test",
"-i", str(file_a),
"-e", "42",
"-q", "-p", "ipc",
"-o", os.path.join(output_folder,
"res.fa")]):
RapidPeptidesGenerator.main()
# Check result
nb_line = 0
with open(os.path.join(output_folder, "res.fa")) as file_res:
for line in file_res:
nb_line += 1
assert line in truth_ipc
assert nb_line == len(truth_ipc)
def test_no_enz(capsys, monkeypatch, list_enz, res_dig_1_42):
""" Test -l behavior """
responses = iter(["1 42", ""])
......@@ -612,6 +1027,19 @@ def test_no_enz(capsys, monkeypatch, list_enz, res_dig_1_42):
assert list_enz in captured.out
assert res_dig_1_42 in captured.out
def test_no_enz_ipc(capsys, monkeypatch, list_enz, res_dig_1_42_ipc):
""" Test -l behavior """
responses = iter(["1 42", ""])
with unittest.mock.patch("sys.argv", ["func_test", "-p", "ipc",
"-s", "DREALDSSWKKLRSgagGRKNAGI"\
"RLVLWMLDFDAHQPDSVLQREFL"]):
monkeypatch.setattr('builtins.input', lambda msg: next(responses))
RapidPeptidesGenerator.main()
# Output
captured = capsys.readouterr()
assert list_enz in captured.out
assert res_dig_1_42_ipc in captured.out
def test_no_enz_quit(capsys, monkeypatch, list_enz):
""" Test -l behavior """
responses = iter(["q"])
......@@ -640,3 +1068,18 @@ def test_no_enz_err(capsys, monkeypatch, list_enz, res_dig_1_42):