/** Test of process method, of class FastaReader. */ @Test public void testProcess() throws Exception { logger.info("process"); InputStream inStream = this.getClass().getResourceAsStream("/PF00104_small.fasta"); assertNotNull(inStream); FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>( inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())); LinkedHashMap<String, ProteinSequence> proteinSequences = fastaReader.process(); inStream.close(); // Should have 282 sequences // logger.debug("Expecting 283 got " + proteinSequences.size()); assertEquals(proteinSequences.size(), 283); int seqNum = 0; for (String id : proteinSequences.keySet()) { ProteinSequence proteinSequence = proteinSequences.get(id); switch (seqNum) { case 0: assertEquals(proteinSequence.getAccession().getID(), "A2D504_ATEGE/1-46"); assertEquals( proteinSequence.getSequenceAsString(), "-----------------FK-N----LP-LED----------------Q----ITL--IQY-----------SWM----------------------CL-SSFA------LSWRSYK---HTNSQFLYFAPDLVF-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"); break; case 281: // logger.debug("Get Accession: {}", proteinSequence.getAccession()); // logger.debug("Get Protein Sequence: {}", proteinSequence.getSequenceAsString()); assertEquals(proteinSequence.getAccession().getID(), "Q9PU76_CRONI/141-323"); assertEquals( proteinSequence.getSequenceAsString(), "VETVTELTEFAKSI-PGFS-N----LD-LND----------------Q----VTL--LKY-----------GVY----------------------EA-IFAM------LASVMNK---DGMPVAYGNGFITRE------------------------------------------------------------------------------------------------------------------------------------------------------------FLKSLRKPFCDIMEPKFDFA-MKF-NSL-E-LDDSDI--------------------SLFVA-AIIC-CGDRPG-------------------------------------------LVNV--GHIEKMQESIVHVLKL-H-----LQN---------NH---PD----------------------------DI------F--------LFP-KLLQKMAD-LRQLV-----------------TEH-AQLV--QIIKK---TESDAHLHPLL-------QEI---"); break; case 282: assertEquals(proteinSequence.getAccession().getID(), "Q98SJ1_CHICK/15-61"); assertEquals( proteinSequence.getSequenceAsString(), "---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q-----------------NW------Q--------RFY-QLTKLLDS-MHDVV-----------------ENL-LSFC--FQTFLDKSM--SIEFPEML-------AEI---"); break; } seqNum++; } assertEquals(seqNum, 283); }
/** Test of process method, of class GenbankReader. */ @Test public void testProcess() throws Throwable { /* * Method 1: With the GenbankProxySequenceReader */ // Try with the GenbankProxySequenceReader GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader = new GenbankProxySequenceReader<AminoAcidCompound>( System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet()); ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader); genbankProteinReader .getHeaderParser() .parseHeader(genbankProteinReader.getHeader(), proteinSequence); logger.info( "Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10)); GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader = new GenbankProxySequenceReader<NucleotideCompound>( System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet()); DNASequence dnaSequence = new DNASequence(genbankDNAReader); genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence); logger.info( "Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10)); /* * Method 2: With the GenbankReaderHelper */ // Try with the GenbankReaderHelper ClasspathResource dnaResource = new ClasspathResource("NM_000266.gb", true); // File dnaFile = new File("src/test/resources/NM_000266.gb"); // File protFile = new File("src/test/resources/BondFeature.gb"); ClasspathResource protResource = new ClasspathResource("BondFeature.gb"); LinkedHashMap<String, DNASequence> dnaSequences = GenbankReaderHelper.readGenbankDNASequence(dnaResource.getInputStream()); for (DNASequence sequence : dnaSequences.values()) { logger.info("DNA Sequence: {}", sequence.getSequenceAsString()); } LinkedHashMap<String, ProteinSequence> protSequences = GenbankReaderHelper.readGenbankProteinSequence(protResource.getInputStream()); for (ProteinSequence sequence : protSequences.values()) { logger.info("Protein Sequence: {}", sequence.getSequenceAsString()); } /* * Method 3: With the GenbankReader Object */ // Try reading with the GanbankReader GenbankReader<DNASequence, NucleotideCompound> dnaReader = new GenbankReader<DNASequence, NucleotideCompound>( dnaResource.getInputStream(), new GenericGenbankHeaderParser<DNASequence, NucleotideCompound>(), new DNASequenceCreator(DNACompoundSet.getDNACompoundSet())); dnaSequences = dnaReader.process(); logger.info("DNA Sequence: {}", dnaSequences); GenbankReader<ProteinSequence, AminoAcidCompound> protReader = new GenbankReader<ProteinSequence, AminoAcidCompound>( protResource.getInputStream(), new GenericGenbankHeaderParser<ProteinSequence, AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())); protSequences = protReader.process(); logger.info("Protein Sequence: {}", protSequences); }
@Test public void processIntTest() throws Exception { logger.info("process(int)"); InputStream inStream = this.getClass().getResourceAsStream("/PF00104_small.fasta"); assertNotNull(inStream); FastaReader<ProteinSequence, AminoAcidCompound> fastaReader = new FastaReader<ProteinSequence, AminoAcidCompound>( inStream, new GenericFastaHeaderParser<ProteinSequence, AminoAcidCompound>(), new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet())); LinkedHashMap<String, ProteinSequence> proteinSequences = fastaReader.process(200); // Should have 200 sequences // logger.debug("Expecting 200 got " + proteinSequences.size()); assertEquals(proteinSequences.size(), 200); int seqNum = 0; for (String id : proteinSequences.keySet()) { ProteinSequence proteinSequence = proteinSequences.get(id); switch (seqNum) { case 0: assertEquals(proteinSequence.getAccession().getID(), "A2D504_ATEGE/1-46"); assertEquals( proteinSequence.getSequenceAsString(), "-----------------FK-N----LP-LED----------------Q----ITL--IQY-----------SWM----------------------CL-SSFA------LSWRSYK---HTNSQFLYFAPDLVF-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------"); break; case 199: assertEquals(proteinSequence.getAccession().getID(), "Q5F0P7_HUMAN/248-428"); assertEquals( proteinSequence.getSequenceAsString(), "DRELVVIIGWAKHI-PGFS-S----LS-LGD----------------Q----MSL--LQS-----------AWM----------------------EI-LILG------IVYRSLP---YDDKLVYAEDYIMD-------------------------------------------------------------------------------------------------------------------------------------------------------------EEHSRLAGLLELYRAILQLV-RRY-KKL-K-VEKEEF--------------------VTLKA-LALA-NSDSMY-------------------------------------------IEDL--EAVQKLQDLLHEALQD-Y-----ELS---------QR---HE----------------------------EP------W--------RTG-KLLLTLPL-LRQTA-----------------AKA-VQHF--YSVKLQGKV--PMH--KLF-------LEM---"); break; } seqNum++; } assertEquals(seqNum, 200); // Should have 83 sequences proteinSequences = fastaReader.process(200); assertEquals(proteinSequences.size(), 83); seqNum = 0; for (String id : proteinSequences.keySet()) { ProteinSequence proteinSequence = proteinSequences.get(id); switch (seqNum) { case 0: assertEquals(proteinSequence.getAccession().getID(), "RARA_CANFA/233-413"); assertEquals( proteinSequence.getSequenceAsString(), "TKCIIKTVEFAKQL-PGFT-T----LT-IAD----------------Q----ITL--LKA-----------ACL----------------------DI-LILR------ICTRYTP---EQDTMTFSEGLTLN-------------------------------------------------------------------------------------------------------------------------------------------------------------RTQMHKAGFGPLTDLVFAFA-NQL-LPL-E-MDDAET--------------------GLLSA-ICLI-CGDRQD-------------------------------------------LEQP--DRVDMLQEPLLEALKV-Y-----VRK---------RR---PS----------------------------RP------H--------MFP-KMLMKITD-LRSIS-----------------AKG-AERV--ITLKMEIPG--SMP--PLI-------QEM---"); break; case 81: // logger.debug(proteinSequence.getAccession()); // logger.debug(proteinSequence.getSequenceAsString()); assertEquals(proteinSequence.getAccession().getID(), "Q9PU76_CRONI/141-323"); assertEquals( proteinSequence.getSequenceAsString(), "VETVTELTEFAKSI-PGFS-N----LD-LND----------------Q----VTL--LKY-----------GVY----------------------EA-IFAM------LASVMNK---DGMPVAYGNGFITRE------------------------------------------------------------------------------------------------------------------------------------------------------------FLKSLRKPFCDIMEPKFDFA-MKF-NSL-E-LDDSDI--------------------SLFVA-AIIC-CGDRPG-------------------------------------------LVNV--GHIEKMQESIVHVLKL-H-----LQN---------NH---PD----------------------------DI------F--------LFP-KLLQKMAD-LRQLV-----------------TEH-AQLV--QIIKK---TESDAHLHPLL-------QEI---"); break; case 82: assertEquals(proteinSequence.getAccession().getID(), "Q98SJ1_CHICK/15-61"); assertEquals( proteinSequence.getSequenceAsString(), "---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q-----------------NW------Q--------RFY-QLTKLLDS-MHDVV-----------------ENL-LSFC--FQTFLDKSM--SIEFPEML-------AEI---"); break; } seqNum++; } assertEquals(seqNum, 83); fastaReader.close(); inStream.close(); }