public void test_bottom_up_PSMs()
{
Sweet.lollipop = new Lollipop();
Sweet.lollipop.et_high_mass_difference = 2;
Sweet.lollipop.et_low_mass_difference = -2;
Sweet.lollipop.neucode_labeled = false;
Sweet.lollipop.carbamidomethylation = false;
Sweet.lollipop.enter_input_files(new string[] { Path.Combine(TestContext.CurrentContext.TestDirectory, "testHits.psmtsv") }, Lollipop.acceptable_extensions[7], Lollipop.file_types[7], Sweet.lollipop.input_files, false);
Sweet.lollipop.enter_input_files(new string[] { Path.Combine(TestContext.CurrentContext.TestDirectory, "uniprot_yeast_test_12entries.xml") }, Lollipop.acceptable_extensions[2], Lollipop.file_types[2], Sweet.lollipop.input_files, false);
Sweet.lollipop.theoretical_database.get_theoretical_proteoforms(TestContext.CurrentContext.TestDirectory);
Assert.AreEqual(10, Sweet.lollipop.theoretical_database.bottom_up_psm_by_accession.Count);
Sweet.lollipop.min_bu_peptides = 0;
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E1");
e.modified_mass = 1816.0128; //Q3E770 - no bottomup-peptides
var relations = Sweet.lollipop.target_proteoform_community.relate(new ExperimentalProteoform[] { e }, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms, ProteoformComparison.ExperimentalTheoretical, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(1, relations.Count);
Sweet.lollipop.min_bu_peptides = 1;
relations = Sweet.lollipop.target_proteoform_community.relate(new ExperimentalProteoform[] { e }, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms, ProteoformComparison.ExperimentalTheoretical, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(0, relations.Count);
e.modified_mass = 29260.9826; //P0CX35
Sweet.lollipop.min_bu_peptides = 1;
relations = Sweet.lollipop.target_proteoform_community.relate(new ExperimentalProteoform[] { e }, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms, ProteoformComparison.ExperimentalTheoretical, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(0, relations.Count); //modified peptide, no mod theoretical with this accession so returns 0
e.modified_mass = 59841.6191; //P32329
relations = Sweet.lollipop.target_proteoform_community.relate(new ExperimentalProteoform[] { e }, Sweet.lollipop.target_proteoform_community.theoretical_proteoforms, ProteoformComparison.ExperimentalTheoretical, TestContext.CurrentContext.TestDirectory, false);
Assert.AreEqual(1, relations.Count);
Assert.AreEqual(0, Proteoform.get_possible_PSMs("Q3E770", new PtmSet(new List <Ptm>()), 3, 20).Count());
Assert.AreEqual(0, Proteoform.get_possible_PSMs("P0CX35", new PtmSet(new List <Ptm>()), 3, 20).Count());
Assert.AreEqual(1, Proteoform.get_possible_PSMs("P0CX35", Sweet.lollipop.theoretical_database.possible_ptmset_dictionary[80].Where(p => p.ptm_description.Contains("Phospho")).First(), 2, 500).Count());
Assert.AreEqual(0, Proteoform.get_possible_PSMs("P0CX35", Sweet.lollipop.theoretical_database.possible_ptmset_dictionary[80].Where(p => p.ptm_description.Contains("Phospho")).First(), 1, 5).Count());
}
public static ProteoformRelation make_relation(Proteoform p1, Proteoform p2, ProteoformComparison c, double delta_mass)
{
ProteoformRelation pp = new ProteoformRelation(p1, p2, c, delta_mass, TestContext.CurrentContext.TestDirectory);
p1.relationships.Add(pp);
p2.relationships.Add(pp);
return(pp);
}
public void TestInitialize()
{
// Myoglobin (Uniprot P68082) with N-terminal methionine removed
string proForma = "GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG";
myo = new Proteoform(proForma);
// Histone H4 (Uniprot P62805) PFR1033
proForma = "S[Acetyl|formula:C2H2O]GRGKGGKGLGKGGAKRHRK[Dimethyl|formula:C2H4]VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG";
h4 = new Proteoform(proForma);
}
public void TestInitialize()
{
// myoglobin
string proForma = "GLSDGEWQQVLNVWGKVEADIAGHGQEVLIRLFTGHPETLEKFDKFKHLKTEAEMKASEDLKKHGTVVLTALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSKHPGDFGADAQGAMTKALELFRNDIAAKYKELGFQG";
Proteoform myo = new Proteoform(proForma);
// create b5 ion
var frag = myo.MakeFragment(5, 'b');
trans = new Transition(myo, frag, 7, 4);
}
//MAKE RELATION
public static void make_relation(Proteoform p1, Proteoform p2)
{
ProteoformRelation pp = new ProteoformRelation(p1, p2, ProteoformComparison.ExperimentalExperimental, 0, TestContext.CurrentContext.TestDirectory);
DeltaMassPeak ppp = new DeltaMassPeak(pp, new HashSet <ProteoformRelation> {
pp
});
pp.peak = ppp;
pp.Accepted = true;
ppp.Accepted = true;
p1.relationships.Add(pp);
p2.relationships.Add(pp);
}
/// <summary>
/// Initializes a Transition instance.
/// </summary>
/// <param name="parent">Proteoform that represents parent ion</param>
/// <param name="frag">Fragment that represents fragment ion</param>
/// <param name="parentCharge">Charge of parent ion</param>
/// <param name="fragCharge">Charge of fragment ion</param>
public Transition(Proteoform parent, Fragment frag, int parentCharge, int fragCharge)
{
// Set member values
this.Precursor = parent;
this.Fragment = frag;
this.PrecursorCharge = parentCharge;
this.FragmentCharge = fragCharge;
// Generate isotopic distributions using the Mercury7 algorithm
IIsotopeDistGenerator gen = new Mercury7();
this.PrecursorDistribution = gen.GenerateChargedIsotopicDistribution(parent.GetFormula(), parentCharge);
this.FragmentDistribution = gen.GenerateChargedIsotopicDistribution(frag.GetFormula(), fragCharge);
}
public void test_distinct_by()
{
Proteoform a = new Proteoform("a");
Proteoform b = new Proteoform("b");
Proteoform c = new Proteoform("c");
Proteoform c1 = new Proteoform("c");
List <Proteoform> z = new List <Proteoform> {
a, b, c, c1
};
z.DistinctBy(p => p.accession);
Assert.AreEqual(4, z.Count);
z = z.DistinctBy(p => p.accession).ToList();
Assert.AreEqual(3, z.Count);
}
public void nodes_table_gives_meaningful_unmodified_theoreticals()
{
Proteoform p = ConstructorsForTesting.make_a_theoretical();
ProteoformFamily f = new ProteoformFamily(p);
f.construct_family();
string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> {
f
},
null,
CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2,
f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]);
Assert.True(node_table.Contains(CytoscapeScript.unmodified_theoretical_label));
Assert.AreNotEqual(f.theoretical_proteoforms[0].accession, CytoscapeScript.get_proteoform_shared_name(p, Lollipop.node_labels[0], 2));
}
public void nodes_table_gives_meaningful_modified_theoreticals2()
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("K", out motif);
Modification m = new Modification("id", _modificationType: "modtype", _target: motif, _locationRestriction: "Anywhere.", _monoisotopicMass: 1);
Proteoform p = ConstructorsForTesting.make_a_theoretical();
ProteoformFamily f = new ProteoformFamily(p);
f.construct_family();
string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> {
f
},
null,
CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2,
f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]);
Assert.True(node_table.Contains(CytoscapeScript.modified_theoretical_label));
Assert.AreNotEqual(f.theoretical_proteoforms[0].accession, CytoscapeScript.get_proteoform_shared_name(p, Lollipop.node_labels[0], 2));
}
public void nodes_table_gives_meaningful_modified_theoreticals2()
{
ModificationMotif motif;
ModificationMotif.TryGetMotif("K", out motif);
ModificationWithMass m = new ModificationWithMass("oxidation", new Tuple <string, string>("", ""), motif, ModificationSites.K, 1, new Dictionary <string, IList <string> >(), new List <double>(), new List <double>(), "");
Proteoform p = ConstructorsForTesting.make_a_theoretical();
ProteoformFamily f = new ProteoformFamily(p);
f.construct_family();
string node_table = CytoscapeScript.get_cytoscape_nodes_tsv(new List <ProteoformFamily> {
f
},
false,
CytoscapeScript.color_scheme_names[0], Lollipop.edge_labels[0], Lollipop.node_labels[0], Lollipop.node_positioning[0], 2,
f.theoretical_proteoforms, false, Lollipop.gene_name_labels[1]);
Assert.True(node_table.Contains(CytoscapeScript.modified_theoretical_label));
Assert.AreNotEqual(f.theoretical_proteoforms[0].accession, CytoscapeScript.get_proteoform_shared_name(p, Lollipop.node_labels[0], 2));
}