Esempio n. 1
0
        public void TestDtaselect()
        {
            string header = "Locus	Sequence Count	Spectrum Count	Sequence Coverage	Length	MolWt	pI	Validation Status	Descriptive Name";
            IPropertyConverter <IIdentifiedProtein> converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(header, '\t');

            Assert.AreEqual(header, converter.Name);

            string             line    = "YDR050C	495	495	81.10%	249	26795.41	5.74	U	YDR050C TPI1 SGDID:S000002457, Chr IV from 556470-555724, reverse complement, Verified ORF, \"Triose phosphate isomerase, abundant glycolytic enzyme; mRNA half-life is regulated by iron availability; transcription is controlled by activators Reb1p, Gcr1p, and Rap1p through binding sites in the 5' non-coding region\"";
            IIdentifiedProtein protein = new IdentifiedProtein();

            converter.SetProperty(protein, line);

            Assert.AreEqual("YDR050C", protein.Name);
            Assert.AreEqual("TPI1 SGDID:S000002457, Chr IV from 556470-555724, reverse complement, Verified ORF, \"Triose phosphate isomerase, abundant glycolytic enzyme; mRNA half-life is regulated by iron availability; transcription is controlled by activators Reb1p, Gcr1p, and Rap1p through binding sites in the 5' non-coding region\"", protein.Description);
            Assert.AreEqual(495, protein.UniquePeptideCount);
            Assert.AreEqual(81.1, protein.Coverage);
            Assert.AreEqual(26795.41, protein.MolecularWeight);
            Assert.AreEqual(5.74, protein.IsoelectricPoint);

            for (int i = 0; i < 495; i++)
            {
                protein.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum()));
            }
            Assert.AreEqual(line, converter.GetProperty(protein));
        }
Esempio n. 2
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        public void TestNoredundant()
        {
            string header = "	Reference	PepCount	UniquePepCount	CoverPercent	MW	PI	IdentifiedName";
            IPropertyConverter <IIdentifiedProtein> converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(header, '\t');

            Assert.AreEqual(header, converter.Name);

            string             line    = "\tIPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088 Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial	84	19	43.46%	61054.43	5.70	IPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088 Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial";
            IIdentifiedProtein protein = new IdentifiedProtein();

            converter.SetProperty(protein, line);


            Assert.AreEqual("IPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088", protein.Name);
            Assert.AreEqual("Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial", protein.Description);
            Assert.AreEqual(19, protein.UniquePeptideCount);
            Assert.AreEqual(43.46, protein.Coverage);
            Assert.AreEqual(61054.43, protein.MolecularWeight);
            Assert.AreEqual(5.7, protein.IsoelectricPoint);

            for (int i = 0; i < 84; i++)
            {
                protein.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum()));
            }
            Assert.AreEqual(line, converter.GetProperty(protein));
        }
Esempio n. 3
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        public void TestNoredundant()
        {
            string header = "\t\"File, Scan(s)\"\tSequence\tMH+\tDiff(MH+)\tCharge\tRank\tScore\tDeltaScore\tExpectValue\tQuery\tIons\tReference\tDIFF_MODIFIED_CANDIDATE\tPI\tMissCleavage\tModification";
            IPropertyConverter <IIdentifiedSpectrum> converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(header, '\t');

            Assert.AreEqual(header, converter.Name);

            IIdentifiedSpectrum mphit = new IdentifiedSpectrum();

            mphit.Query.FileScan.ShortFileName = "AAA,1-2";

            IdentifiedPeptide mp1 = new IdentifiedPeptide(mphit);

            mp1.Sequence = "AAAAA";
            mp1.AddProtein("PROTEIN1");
            mp1.AddProtein("PROTEIN2");

            IdentifiedPeptide mp2 = new IdentifiedPeptide(mphit);

            mp2.Sequence = "BBBBB";
            mp2.AddProtein("PROTEIN3");

            mphit.TheoreticalMH      = 1000.00102;
            mphit.ExperimentalMH     = 1000.0;
            mphit.Query.Charge       = 2;
            mphit.Rank               = 1;
            mphit.Score              = 100.2;
            mphit.DeltaScore         = 0.5;
            mphit.ExpectValue        = 1.1e-2;
            mphit.Query.QueryId      = 10;
            mphit.NumMissedCleavages = 1;
            mphit.Modifications      = "O18(1)";

            string expect = "	AAA,1 - 2	AAAAA ! BBBBB	1000.00102	0.00102	2	1	100.2	0.5	1.10E-002	10	0|0	PROTEIN1/PROTEIN2 ! PROTEIN3		0.00	1	O18(1)";

            Assert.AreEqual(expect, converter.GetProperty(mphit));

            string expectNew = "	BBB,2 - 3	BBBBB	1002.00783	-0.00200	3	2	200.2	0.6	1.20E-003	20	0|0	PROTEIN2/PROTEIN4		0.00	2	O18(2)";

            converter.SetProperty(mphit, expectNew);
            Assert.AreEqual(expectNew, converter.GetProperty(mphit));
        }
Esempio n. 4
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 public override string GetProperty(T t)
 {
     return(baseConverter.GetProperty(t));
 }