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Commit 04f02f0f authored by Nicolas MAILLET's avatar Nicolas MAILLET
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Revert "Adaptive precision for masses - tests" 

This reverts commit c6c92a00.

Back to 5 precisons digit for avg masses
parent fd26b8d1
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tests/test_core.py
+ 45
− 45
View file @ 04f02f0f
......@@ -91,12 +91,12 @@ def test_output_results(capsys, tmp_path):
assert out == outf.read()
assert out == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.20742672,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.112129335,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.196527685,3."\
"14,FZQSD\nInput,3,fake_enzyme1,15,3,349.112129335"\
",3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"078978645,5.97,F\n"
"Input,0,fake_enzyme1,4,4,534.20743,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.11213,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.19653,3."\
"14,FZQSD\nInput,3,fake_enzyme1,15,3,349.112"\
"13,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"07898,5.97,F\n"
# CSV output
seq = "WQSDESDFZQSDESDF"
......@@ -115,12 +115,12 @@ def test_output_results(capsys, tmp_path):
assert out == outf.read()
assert out == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.526,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.2976,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.4894,3."\
"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"\
"6,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"1919,5.97,F\n"
"58,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"19188,5.97,F\n"
# TSV output
output_file = tmp_path.joinpath("test_result.tsv")
......@@ -134,12 +134,12 @@ def test_output_results(capsys, tmp_path):
assert out == "Original_header\tNo_peptide\tEnzyme\tCleavi"\
"ng_pos\tPeptide_size\tPeptide_mass\tpI\tSeq"\
"uence\nInput\t0\tfake_enzyme1\t4\t4\t534.52"\
"6\t3.14\tWQSD\nInput\t1\tfake_enzyme1\t7"\
"\t3\t349.2976\t3.04\tESD\nInput\t2\tfake_e"\
"nzyme1\t12\t5\t495.4894\t3.14\tFZQSD\nInpu"\
"t\t3\tfake_enzyme1\t15\t3\t349.2976\t3.04"\
"598\t3.14\tWQSD\nInput\t1\tfake_enzyme1\t7"\
"\t3\t349.29758\t3.04\tESD\nInput\t2\tfake_e"\
"nzyme1\t12\t5\t495.48938\t3.14\tFZQSD\nInpu"\
"t\t3\tfake_enzyme1\t15\t3\t349.29758\t3.04"\
"\tESD\nInput\t4\tfake_enzyme1\t16\t1\t165.1"\
"919\t5.97\tF\n"
"9188\t5.97\tF\n"
# Fasta output
output_file = tmp_path.joinpath("test_result.fasta")
......@@ -150,12 +150,12 @@ def test_output_results(capsys, tmp_path):
out, err = capsys.readouterr()
with open(output_file, encoding="utf-8") as outf:
assert out == outf.read()
assert out == ">Input_0_fake_enzyme1_4_4_534.526_3.14\nW"\
"QSD\n>Input_1_fake_enzyme1_7_3_349.2976_3."\
assert out == ">Input_0_fake_enzyme1_4_4_534.52598_3.14\nW"\
"QSD\n>Input_1_fake_enzyme1_7_3_349.29758_3."\
"04\nESD\n>Input_2_fake_enzyme1_12_5_495.489"\
"4_3.14\nFZQSD\n>Input_3_fake_enzyme1_15_3_"\
"349.2976_3.04\nESD\n>Input_4_fake_enzyme1_"\
"16_1_165.1919_5.97\nF\n"
"38_3.14\nFZQSD\n>Input_3_fake_enzyme1_15_3_"\
"349.29758_3.04\nESD\n>Input_4_fake_enzyme1_"\
"16_1_165.19188_5.97\nF\n"
# CSV output in quiet
seq = "WQSDESDFZQSDESDF"
......@@ -173,12 +173,12 @@ def test_output_results(capsys, tmp_path):
with open(output_file, encoding="utf-8") as outf:
assert outf.read() == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.526,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.2976,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.4894,3."\
"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"\
"6,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"1919,5.97,F\n"
"58,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"19188,5.97,F\n"
# CSV output in verbose > 2
seq = "WQSDESDFZQSDESDF"
......@@ -195,12 +195,12 @@ def test_output_results(capsys, tmp_path):
content = outf.read()
assert content == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.526,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.2976,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.4894,3."\
"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"\
"6,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"1919,5.97,F\n"
"58,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"19188,5.97,F\n"
# Verbose > 2
assert out == "\nNumber of cleavage: 4\nCleavage position: 4, 7, 12, 15\n"\
"Number of miscleavage: 0\nmiscleavage position: \nmis"\
......@@ -221,12 +221,12 @@ def test_output_results(capsys, tmp_path):
"al peptide: WQSD\nC terminal peptide: F\nOriginal_header,"\
"No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.526,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.2976,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.4894,3."\
"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"\
"6,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"1919,5.97,F\n"
"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
......@@ -238,12 +238,12 @@ def test_output_results(capsys, tmp_path):
out, err = capsys.readouterr()
assert out == "Original_header,No_peptide,Enzyme,Cleaving_"\
"pos,Peptide_size,Peptide_mass,pI,Sequence\n"\
"Input,0,fake_enzyme1,4,4,534.526,3.14,WQS"\
"D\nInput,1,fake_enzyme1,7,3,349.2976,3.04,"\
"ESD\nInput,2,fake_enzyme1,12,5,495.4894,3."\
"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"\
"6,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"1919,5.97,F\n"
"58,3.04,ESD\nInput,4,fake_enzyme1,16,1,165."\
"19188,5.97,F\n"
def test_peptide():
"""Test class 'Peptide'"""
......@@ -258,7 +258,7 @@ def test_peptide():
print_res = pep0.__repr__()
assert print_res == "Original header: Test\nNo. peptide: 1\nEnzyme: fake_"\
"enzyme\nCleav. pos: 3\nPep. size: 8\nPep. mass: 1012"\
".9849\npKa values from: IPC\nPep. pI: 2.91\nSequenc"\
".98488\npKa values from: IPC\nPep. pI: 2.91\nSequenc"\
"e: QWSDESDF\n"
# Test function '__eq__()'
......@@ -279,12 +279,12 @@ def test_peptide():
# Test function '__format__()'
format_res = pep0.__format__("csv")
assert format_res == "Test,1,fake_enzyme,3,8,1012.9849,2.91,QWSDESDF"
assert format_res == "Test,1,fake_enzyme,3,8,1012.98488,2.91,QWSDESDF"
format_res = pep2.__format__("tsv")
assert format_res == "Test\t1\tfake_enzyme\t2\t8\t1012.9849\t2.91\tQWSD"\
assert format_res == "Test\t1\tfake_enzyme\t2\t8\t1012.98488\t2.91\tQWSD"\
"ESDF"
format_res = pep3.__format__("fasta")
assert format_res == ">Test_2_fake_enzyme_3_8_1012.9849_2.91\nQWSDESDF"
assert format_res == ">Test_2_fake_enzyme_3_8_1012.98488_2.91\nQWSDESDF"
# Test function 'def get_isoelectric_point():'
assert pep3.get_isoelectric_point() == 2.91
......
......
tests/test_digest.py
+ 25
− 25
View file @ 04f02f0f
......@@ -29,12 +29,12 @@ def test_resultonedigestion():
"]\nRatio of miscleavage: 66.666666666666"\
"66\nPeptides: [Original header: Test\nNo. "\
"peptide: 0\nEnzyme: fake_enzyme\nCleav. po"\
"s: 3\nPep. size: 8\nPep. mass: 1012.9849"\
"s: 3\nPep. size: 8\nPep. mass: 1012.98488"\
"\npKa values from: IPC\nPep. pI: 2.91\nSeq"\
"uence: QWSDESDF\n, Original header: Test\n"\
"No. peptide: 1\nEnzyme: fake_enzyme\nCleav"\
". pos: 4\nPep. size: 8\nPep. mass: 1012.98"\
"49\npKa values from: IPC\nPep. pI: 2.91\n"\
"488\npKa values from: IPC\nPep. pI: 2.91\n"\
"Sequence: QWSDESDF\n]\n"
# Test function '__eq__()'
......@@ -59,15 +59,15 @@ def test_resultonedigestion():
# Test function '__format__()'
format_res = res_dig0.__format__("csv")
assert format_res == "Test,0,fake_enzyme,3,8,1012.9849,2.91,QWSDESDF\nTe"\
"st,1,fake_enzyme,4,8,1012.9849,2.91,QWSDESDF\n"
assert format_res == "Test,0,fake_enzyme,3,8,1012.98488,2.91,QWSDESDF\nTe"\
"st,1,fake_enzyme,4,8,1012.98488,2.91,QWSDESDF\n"
format_res = res_dig0.__format__("tsv")
assert format_res == "Test\t0\tfake_enzyme\t3\t8\t1012.9849\t2.91\tQWSDE"\
"SDF\nTest\t1\tfake_enzyme\t4\t8\t1012.9849\t2.91\t"\
assert format_res == "Test\t0\tfake_enzyme\t3\t8\t1012.98488\t2.91\tQWSDE"\
"SDF\nTest\t1\tfake_enzyme\t4\t8\t1012.98488\t2.91\t"\
"QWSDESDF\n"
format_res = res_dig0.__format__("fasta")
assert format_res == ">Test_0_fake_enzyme_3_8_1012.9849_2.91\nQWSDESDF\n"\
">Test_1_fake_enzyme_4_8_1012.9849_2.91\nQWSDESDF\n"
assert format_res == ">Test_0_fake_enzyme_3_8_1012.98488_2.91\nQWSDESDF\n"\
">Test_1_fake_enzyme_4_8_1012.98488_2.91\nQWSDESDF\n"
# Test function 'pop_peptides()'
assert res_dig5.peptides != []
......@@ -374,24 +374,24 @@ def test_digest_from_input(capsys, tmp_path):
"\nRatio of miscleavage: 0.0\nPeptides: "\
"[Original header: Input\nNo. peptide: 0"\
"\nEnzyme: fake_enzyme1\nCleav. pos: 4\nPe"\
"p. size: 4\nPep. mass: 534.526\npKa val"\
"p. size: 4\nPep. mass: 534.52598\npKa val"\
"ues from: IPC\nPep. pI: 3.14\nSequence: W"\
"QSD\n, Original header: Input\nNo. peptid"\
"e: 1\nEnzyme: fake_enzyme1\nCleav. pos: 7"\
"\nPep. size: 3\nPep. mass: 349.2976\npKa"\
"\nPep. size: 3\nPep. mass: 349.29758\npKa"\
" values from: IPC\nPep. pI: 3.04\nSequenc"\
"e: ESD\n, Original header: Input\nNo. pep"\
"tide: 2\nEnzyme: fake_enzyme1\nCleav. pos"\
": 12\nPep. size: 5\nPep. mass: 495.4894"\
": 12\nPep. size: 5\nPep. mass: 495.48938"\
"\npKa values from: IPC\nPep. pI: 3.14\nSe"\
"quence: FZQSD\n, Original header: Input\n"\
"No. peptide: 3\nEnzyme: fake_enzyme1\nCle"\
"av. pos: 15\nPep. size: 3\nPep. mass: 349"\
".2976\npKa values from: IPC\nPep. pI: 3."\
".29758\npKa values from: IPC\nPep. pI: 3."\
"04\nSequence: ESD\n, Original header: Inp"\
"ut\nNo. peptide: 4\nEnzyme: fake_enzyme1"\
"\nCleav. pos: 16\nPep. size: 1\nPep. mass"\
": 165.1919\npKa values from: IPC\nPep. p"\
": 165.19188\npKa values from: IPC\nPep. p"\
"I: 5.97\nSequence: F\n]\n"
# Test wrong input data
......@@ -414,31 +414,31 @@ def test_digest_from_input(capsys, tmp_path):
"\nRatio of miscleavage: 0.0\nPeptides: "\
"[Original header: Fake1\nNo. peptide: 0\n"\
"Enzyme: fake_enzyme1\nCleav. pos: 4\nPep."\
" size: 4\nPep. mass: 534.526\npKa value"\
" 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: 349.2976\npKa v"\
"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: 495.4894\np"\
"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"\
"76\npKa values from: IPC\nPep. pI: 3.04"\
"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"\
"65.1919\npKa values from: IPC\nPep. pI: "\
"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 miscleav"\
"age: 0\nPositions of miscleavage: []\nRat"\
"io of miscleavage: 0\nPeptides: [Original"\
" header: Fake2\nNo. peptide: 0\nEnzyme: f"\
"ake_enzyme1\nCleav. pos: 0\nPep. size: 15"\
"\nPep. mass: 2014.351\npKa values from:"\
"\nPep. mass: 2014.35098\npKa values from:"\
" IPC\nPep. pI: 7.16\nSequence: NPHARDORCO"\
"MPLET\n]\n"
......@@ -456,31 +456,31 @@ def test_digest_from_input(capsys, tmp_path):
"\nRatio of miscleavage: 0.0\nPeptides: "\
"[Original header: Fake1\nNo. peptide: 0\n"\
"Enzyme: fake_enzyme1\nCleav. pos: 4\nPep."\
" size: 4\nPep. mass: 534.526\npKa value"\
" 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: 349.2976\npKa v"\
"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: 495.4894\np"\
"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"\
"76\npKa values from: IPC\nPep. pI: 3.04"\
"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"\
"65.1919\npKa values from: IPC\nPep. pI: "\
"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: 2014.351\npKa value"\
"ize: 15\nPep. mass: 2014.35098\npKa value"\
"s from: IPC\nPep. pI: 7.16\nSequence: NPH"\
"ARDORCOMPLET\n]\n")
assert len(res) == 2
......
......
tests/test_functional.py
+ 379
− 379
View file @ 04f02f0f
This diff is collapsed.
tests/test_sequence.py
+ 1
− 1
View file @ 04f02f0f
......@@ -19,7 +19,7 @@ def test_peptide():
# Test function '__repr__()'
assert pep0.__repr__() == "Original header: fake_sequence\nNo. peptide: "\
"42\nEnzyme: Pwet\nCleav. pos: 0\nPep. size: 8"\
"\nPep. mass: 1012.9849\npKa values from: IPC"\
"\nPep. mass: 1012.98488\npKa values from: IPC"\
"\nPep. pI: 2.91\nSequence: QWSDESDF\n"
header = "fake_sequence"
......
......
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