datamodel/compbio/data/sequence/FastaReader.java

   1 package compbio.data.sequence;\r
   2 \r
   3 import java.io.File;\r
   4 import java.io.FileNotFoundException;\r
   5 import java.util.Iterator;\r
   6 import java.util.Scanner;\r
   7 \r
   8 import compbio.util.Util;\r
   9 \r
  10 /**\r
  11  * Reads files with FASTA formatted sequences. All the information in the FASTA\r
  12  * header is preserved including trailing white spaces. All the white spaces are\r
  13  * removed from the sequence.\r
  14  * \r
  15  * Examples of the correct input:\r
  16  * \r
  17  * <pre>\r
  18  * \r
  19  * >zedpshvyzg\r
  20  * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD\r
  21  * \r
  22  * >xovkactesa\r
  23  * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM\r
  24  * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG\r
  25  * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH\r
  26  * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC\r
  27  * \r
  28  * >ntazzewyvv\r
  29  * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD\r
  30  * EASINM       AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      \r
  31  * EFITEA       WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW \r
  32  *   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    \r
  33  *   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   \r
  34  *   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI\r
  35  * \r
  36  *    > 12 d t y wi             k       jbke    \r
  37  *   KLSHHDCD\r
  38  *    N\r
  39  *     H\r
  40  *     HSKCTEPHCGNSHQMLHRDP\r
  41  *     CCDQCQSWEAENWCASMRKAILF\r
  42  * \r
  43  * </pre>\r
  44  * \r
  45  * @author Peter Troshin\r
  46  * @version 1.0 April 2011\r
  47  * \r
  48  */\r
  49 public class FastaReader implements Iterator<FastaSequence> {\r
  50 \r
  51         private final Scanner input;\r
  52 \r
  53         /**\r
  54          * Header data can contain non-ASCII symbols and read in UTF8\r
  55          * \r
  56          * @param input\r
  57          *            the file containing the list of FASTA formatted sequences to\r
  58          *            read from\r
  59          * @throws FileNotFoundException\r
  60          *             if the input file is not found\r
  61          * @throws IllegalStateException\r
  62          *             if the close method was called on this instance\r
  63          * \r
  64          */\r
  65         public FastaReader(final String inputFile) throws FileNotFoundException {\r
  66                 input = new Scanner(new File(inputFile), "UTF8");\r
  67                 input.useDelimiter("\\s*>");\r
  68                 Runtime.getRuntime().addShutdownHook(new Thread() {\r
  69 \r
  70                         @Override\r
  71                         public void run() {\r
  72                                 if (input != null) {\r
  73                                         input.close();\r
  74                                 }\r
  75                         }\r
  76                 });\r
  77         }\r
  78         /**\r
  79          * {@inheritDoc}\r
  80          * \r
  81          * @throws IllegalStateException\r
  82          *             if the close method was called on this instance\r
  83          */\r
  84         @Override\r
  85         public boolean hasNext() {\r
  86                 return input.hasNext();\r
  87         }\r
  88 \r
  89         /**\r
  90          * Reads the next FastaSequence from the input\r
  91          * \r
  92          * @throws AssertionError\r
  93          *             if the header or the sequence is missing\r
  94          * @throws IllegalStateException\r
  95          *             if the close method was called on this instance\r
  96          */\r
  97         @Override\r
  98         public FastaSequence next() {\r
  99                 return FastaReader.toFastaSequence(input.next());\r
 100         }\r
 101 \r
 102         /**\r
 103          * Not implemented\r
 104          */\r
 105         @Override\r
 106         public void remove() {\r
 107                 throw new UnsupportedOperationException();\r
 108         }\r
 109 \r
 110         /**\r
 111          * Call this method to close the connection to the input file if you want to\r
 112          * free up the resources. The connection will be closed on the JVM shutdown\r
 113          * if this method was not called explicitly. No further reading on this\r
 114          * instance of the FastaReader will be possible after calling this method.\r
 115          */\r
 116         public void close() {\r
 117                 input.close();\r
 118         }\r
 119 \r
 120         private static FastaSequence toFastaSequence(final String singleFastaEntry) {\r
 121                 final Scanner sc = new Scanner(singleFastaEntry);\r
 122                 // Use new line delimiter\r
 123                 sc.useDelimiter("\n");\r
 124                 if (!sc.hasNext()) {\r
 125                         throw new AssertionError(\r
 126                                         "The FASTA sequence must contain the header information"\r
 127                                                         + " separated by the new line from the sequence. Given sequence does not appear to "\r
 128                                                         + "contain the header! Given data:\n "\r
 129                                                         + singleFastaEntry);\r
 130                 }\r
 131                 String header = sc.next();\r
 132                 // Get rid of the new line chars (should cover common cases)\r
 133                 header = header.replaceAll("\n", "").replaceAll("\r", "");\r
 134 \r
 135                 sc.useDelimiter("\\s*");\r
 136                 final StringBuilder sb = new StringBuilder();\r
 137                 while (sc.hasNext()) {\r
 138                         sb.append(sc.next().trim());\r
 139                 }\r
 140                 final String sequence = sb.toString();\r
 141                 if (Util.isEmpty(sequence)) {\r
 142                         throw new AssertionError(\r
 143                                         "Empty sequences are not allowed! Please make sure the "\r
 144                                                         + " data is in the FASTA format! Given data:\n "\r
 145                                                         + singleFastaEntry);\r
 146                 }\r
 147                 return new FastaSequence(header, sequence);\r
 148         }\r
 149 }\r