public void results_decoy_dataframe_with_something()
{
Sweet.lollipop = new Lollipop();
Sweet.lollipop.input_files.Add(ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Identification, "n", "s", "1", "1", "1")); //0
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E1");
e.linked_proteoform_references = new List <Proteoform>(new List <Proteoform> {
ConstructorsForTesting.make_a_theoretical()
});
e.ptm_set = e.linked_proteoform_references.Last().ptm_set;
ProteoformFamily f = new ProteoformFamily(e);
f.construct_family();
Sweet.lollipop.decoy_proteoform_communities.Add("Decoy1", new ProteoformCommunity());
Sweet.lollipop.decoy_proteoform_communities["Decoy1"].families = new List <ProteoformFamily> {
f
};
var time_stamp = Sweet.time_stamp();
var directory = TestContext.CurrentContext.TestDirectory;
ResultsSummaryGenerator.save_all(TestContext.CurrentContext.TestDirectory, time_stamp, Sweet.lollipop.TusherAnalysis1 as IGoAnalysis, Sweet.lollipop.TusherAnalysis1 as TusherAnalysis);
Assert.IsTrue(File.Exists(Path.Combine(directory, "decoy_experimental_results_" + time_stamp + ".tsv")));
var lines = File.ReadAllLines(Path.Combine(directory, "decoy_experimental_results_" + time_stamp + ".tsv"));
Assert.AreEqual(2, lines.Length);
}
public void biorepintensitytableLog2Fold()
{
Sweet.lollipop = new Lollipop();
Dictionary <string, List <string> > conditionsBioReps = new Dictionary <string, List <string> >
{
{ "n", new List <string> {
1.ToString(), 2.ToString(), 3.ToString()
} },
{ "s", new List <string> {
1.ToString(), 2.ToString(), 3.ToString()
} },
};
Sweet.lollipop.Log2FoldChangeAnalysis.conditionBiorepIntensitySums = conditionsBioReps.SelectMany(kv => kv.Value.Select(v => new Tuple <string, string>(kv.Key, v))).ToDictionary(t => t, t => 1d);
List <InputFile> input_files = new List <InputFile>
{
ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Quantification, "n", "s", "1", "1", "1"), //0
ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Quantification, "n", "s", "1", "2", "1"), //1
ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Quantification, "n", "s", "2", "1", "1"), //2
ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Quantification, "n", "s", "2", "2", "1"), //3
ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Quantification, "n", "s", "3", "1", "1"), //4
ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Quantification, "n", "s", "3", "2", "1"), //5
};
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("asdf");
e.quant.Log2FoldChangeValues.allIntensities = new Dictionary <Tuple <string, string>, BiorepIntensity>
{
{ new Tuple <string, string>("n", 1.ToString()), new BiorepIntensity(false, 1.ToString(), "n", 1) },
{ new Tuple <string, string>("n", 2.ToString()), new BiorepIntensity(true, 2.ToString(), "n", 1) },
{ new Tuple <string, string>("n", 3.ToString()), new BiorepIntensity(false, 3.ToString(), "n", 1) },
{ new Tuple <string, string>("s", 1.ToString()), new BiorepIntensity(false, 1.ToString(), "s", 1) },
{ new Tuple <string, string>("s", 2.ToString()), new BiorepIntensity(false, 2.ToString(), "s", 1) },
{ new Tuple <string, string>("s", 3.ToString()), new BiorepIntensity(false, 3.ToString(), "s", 1) },
};
// With imputation uses processed values
Assert.False(ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.biological_replicate_intensities(Sweet.lollipop.Log2FoldChangeAnalysis, new List <ExperimentalProteoform> {
e
}, input_files, conditionsBioReps, true, true)).Contains("NaN"));
// Without imputation uses raw values
e.biorepIntensityList = e.quant.Log2FoldChangeValues.allIntensities.Values.Where(x => !x.imputed).ToList();
Assert.True(ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.biological_replicate_intensities(Sweet.lollipop.Log2FoldChangeAnalysis, new List <ExperimentalProteoform> {
e
}, input_files, conditionsBioReps, false, true)).Contains("\t0\t"));
// Headers should be condition_biorep_fraction_techrep
string[] header = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.biological_replicate_intensities(Sweet.lollipop.Log2FoldChangeAnalysis, new List <ExperimentalProteoform> {
e
}, input_files, conditionsBioReps, false, true)).Split('\n')[0].Split('\t');
Assert.True(header[1] == "n_1" && header[2] == "n_2" && header[3] == "n_3" && header[4] == "s_1" && header[5] == "s_2" && header[6] == "s_3");
string[] line = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.biological_replicate_intensities(Sweet.lollipop.Log2FoldChangeAnalysis, new List <ExperimentalProteoform> {
e
}, input_files, conditionsBioReps, false, true)).Split('\n')[1].Split('\t');
Assert.True(line.First() == e.accession);
Assert.True(line[1] == "1" && line[2] == "0" && line[3] == "1" && line[4] == "1" && line[5] == "1" && line[6] == "1"); // all "n" condition is imputed
}
public void test_filter()
{
List <object> asdf = new List <object>();
asdf.Add(ConstructorsForTesting.get_modWithMass("asdf", 0));
asdf.Add(ConstructorsForTesting.get_modWithMass("asd", 0));
asdf.Add(ConstructorsForTesting.get_modWithMass("asdf", 0));
asdf.Add(ConstructorsForTesting.InputFile(@"fake.txt", Labeling.NeuCode, Purpose.CalibrationIdentification, "", "", "1", "1", "1"));
asdf.Add(ConstructorsForTesting.InputFile(@"ake.txt", Labeling.NeuCode, Purpose.CalibrationIdentification, "", "", "1", "1", "1"));
Assert.AreEqual(5, asdf.Count);
Assert.AreEqual(3, ExtensionMethods.filter(asdf, "f").Count());
}
public void results_dataframe_with_something()
{
Sweet.lollipop = new Lollipop();
Sweet.lollipop.input_files.Add(ConstructorsForTesting.InputFile("fake.txt", Labeling.NeuCode, Purpose.Identification, "n", "s", "1", "1", "1")); //0
ExperimentalProteoform e = ConstructorsForTesting.ExperimentalProteoform("E1");
e.linked_proteoform_references = new List <Proteoform>(new List <Proteoform> {
ConstructorsForTesting.make_a_theoretical()
});
e.ptm_set = e.linked_proteoform_references.Last().ptm_set;
ProteoformFamily f = new ProteoformFamily(e);
f.construct_family();
Sweet.lollipop.target_proteoform_community.families = new List <ProteoformFamily> {
f
};
string[] lines = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.experimental_results_dataframe(Sweet.lollipop.target_proteoform_community, Sweet.lollipop.TusherAnalysis1)).Split(new string[] { Environment.NewLine }, StringSplitOptions.None);
Assert.True(lines.Count() == 3);
Assert.True(lines.Any(a => a.Contains("E1")));
TopDownProteoform td = ConstructorsForTesting.TopDownProteoform("TD1", 1000, 10);
td.linked_proteoform_references = new List <Proteoform>(new List <Proteoform> {
ConstructorsForTesting.make_a_theoretical()
});
td.ptm_set = e.linked_proteoform_references.Last().ptm_set;
ProteoformFamily f2 = new ProteoformFamily(td);
f2.construct_family();
Sweet.lollipop.target_proteoform_community.families = new List <ProteoformFamily> {
f2
};
Sweet.lollipop.topdown_proteoforms = new List <TopDownProteoform>()
{
td
};
lines = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.experimental_results_dataframe(Sweet.lollipop.target_proteoform_community, Sweet.lollipop.TusherAnalysis1)).Split(new string[] { Environment.NewLine }, StringSplitOptions.None);
Assert.True(lines.Count() == 3);
lines = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.topdown_results_dataframe()).Split(new string[] { Environment.NewLine }, StringSplitOptions.None);
Assert.True(lines.Count() == 3);
Assert.True(lines.Any(a => a.Contains("TD1")));
Sweet.lollipop.target_proteoform_community.families = new List <ProteoformFamily> {
f, f2
};
lines = ResultsSummaryGenerator.datatable_tostring(ResultsSummaryGenerator.experimental_intensities_dataframe()).Split(new string[] { Environment.NewLine }, StringSplitOptions.None);
Assert.AreEqual(lines.Count(), 4);
Assert.True(lines.Any(a => a.Contains("E1")));
Assert.True(lines.Any(a => a.Contains("TD1")));
}