testsrc/compbio/data/sequence/FastaReaderTester.java

   1 package compbio.data.sequence;\r
   2 \r
   3 import java.io.FileInputStream;\r
   4 import java.io.FileNotFoundException;\r
   5 import java.io.IOException;\r
   6 import java.util.ArrayList;\r
   7 import java.util.List;\r
   8 \r
   9 import org.testng.Assert;\r
  10 import org.testng.annotations.Test;\r
  11 \r
  12 import compbio.metadata.AllTestSuit;\r
  13 \r
  14 public class FastaReaderTester {\r
  15 \r
  16         static FastaSequence s0 = new FastaSequence(\r
  17                         "zedpshvyzg",\r
  18                         "GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD");\r
  19 \r
  20         static FastaSequence s1 = new FastaSequence(\r
  21                         "xovkactesa",\r
  22                         "CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM"\r
  23                                         + "FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG"\r
  24                                         + "FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH"\r
  25                                         + "DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC");\r
  26         static FastaSequence s2 = new FastaSequence(\r
  27                         "ntazzewyvv",\r
  28                         "CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD"\r
  29                                         + "EASINM       AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG"\r
  30                                         + "EFITEA       WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW"\r
  31                                         + " RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    "\r
  32                                         + "W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   "\r
  33                                         + "FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI");\r
  34         static FastaSequence s3 = new FastaSequence(" 12 d t y wi               k       jbke    ",\r
  35                         "  KLSHHDCD" + "   N" + "    H" + "    HSKCTEPHCGNSHQML\n\rHRDP"\r
  36                                         + "    CCDQCQSWEAENWCASMRKAILF");\r
  37         static FastaSequence s4 = new FastaSequence(" 12 d t>y wi->foo          k       jbke    ",\r
  38                         "  KLSHHDCD" + "   N" + "    H" + "    HSKCTEPHCGNSHQML\n\rHRDP"\r
  39                                         + "    CCDQCQSWEAENWCASMRKAILF");\r
  40         @Test()\r
  41         public void test() {\r
  42 \r
  43                 List<FastaSequence> old_seqs = null;\r
  44                 final List<FastaSequence> list = new ArrayList<FastaSequence>();\r
  45                 try {\r
  46                         old_seqs = SequenceUtil.readFasta(new FileInputStream(\r
  47                                         AllTestSuit.TEST_DATA_PATH + "complicated.fasta"));\r
  48                         final FastaReader fr = new FastaReader(AllTestSuit.TEST_DATA_PATH\r
  49                                         + "complicated.fasta");\r
  50 \r
  51                         while (fr.hasNext()) {\r
  52                                 final FastaSequence fs = fr.next();\r
  53                                 list.add(fs);\r
  54                         }\r
  55                 } catch (final FileNotFoundException e) {\r
  56                         e.printStackTrace();\r
  57                         Assert.fail(e.getLocalizedMessage());\r
  58                 } catch (final IOException e) {\r
  59                         e.printStackTrace();\r
  60                         Assert.fail(e.getLocalizedMessage());\r
  61                 }\r
  62                 System.out.println("OLD: " + old_seqs);\r
  63                 System.out.println("NEW: " + list);\r
  64                 Assert.assertEquals(old_seqs.size(), list.size());\r
  65                 Assert.assertEquals(old_seqs.get(0), list.get(0));\r
  66                 Assert.assertEquals(old_seqs.get(1), list.get(1));\r
  67                 // Assert.assertEquals(old_seqs.get(2), list.get(2));\r
  68                 // Assert.assertEquals(seqs.get(3), list.get(3));\r
  69 \r
  70                 Assert.assertEquals(FastaReaderTester.s0, list.get(0));\r
  71                 Assert.assertEquals(FastaReaderTester.s1, list.get(1));\r
  72                 Assert.assertEquals(FastaReaderTester.s2, list.get(2));\r
  73                 Assert.assertEquals(FastaReaderTester.s3, list.get(3));\r
  74                 Assert.assertEquals(FastaReaderTester.s4, list.get(4));\r
  75 \r
  76         }\r
  77 }\r