datamodel/compbio/data/sequence/FastaReader.java

   1 /* Copyright (c) 2011 Peter Troshin\r
   2  *  \r
   3  *  JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0\r
   4  * \r
   5  *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
   6  *  Apache License version 2 as published by the Apache Software Foundation\r
   7  * \r
   8  *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
   9  *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
  10  *  License for more details.\r
  11  * \r
  12  *  A copy of the license is in apache_license.txt. It is also available here:\r
  13  * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
  14  * \r
  15  * Any republication or derived work distributed in source code form\r
  16  * must include this copyright and license notice.\r
  17  */\r
  18 package compbio.data.sequence;\r
  19 \r
  20 import java.io.File;\r
  21 import java.io.FileNotFoundException;\r
  22 import java.io.InputStream;\r
  23 import java.util.Iterator;\r
  24 import java.util.Scanner;\r
  25 import java.util.regex.MatchResult;\r
  26 \r
  27 import javax.vecmath.MismatchedSizeException;\r
  28 \r
  29 import compbio.util.Util;\r
  30 \r
  31 /**\r
  32  * Reads files with FASTA formatted sequences. All the information in the FASTA\r
  33  * header is preserved including trailing white spaces. All the white spaces are\r
  34  * removed from the sequence.\r
  35  * \r
  36  * Examples of the correct input:\r
  37  * \r
  38  * <pre>\r
  39  * \r
  40  * >zedpshvyzg\r
  41  * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD\r
  42  * \r
  43  * >xovkactesa\r
  44  * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM\r
  45  * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG\r
  46  * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH\r
  47  * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC\r
  48  * \r
  49  * >ntazzewyvv\r
  50  * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD\r
  51  * EASINM       AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      \r
  52  * EFITEA       WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW \r
  53  *   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    \r
  54  *   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   \r
  55  *   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI\r
  56  * \r
  57  *    > 12 d t y wi             k       jbke    \r
  58  *   KLSHHDCD\r
  59  *    N\r
  60  *     H\r
  61  *     HSKCTEPHCGNSHQMLHRDP\r
  62  *     CCDQCQSWEAENWCASMRKAILF\r
  63  * \r
  64  * </pre>\r
  65  * \r
  66  * @author Peter Troshin\r
  67  * @version 1.0 April 2011\r
  68  * \r
  69  */\r
  70 public class FastaReader implements Iterator<FastaSequence> {\r
  71 \r
  72         private final Scanner input;\r
  73         /**\r
  74          * Delimiter for the scanner\r
  75          */\r
  76         private final String DELIM=">";\r
  77         /**\r
  78          * Header data can contain non-ASCII symbols and read in UTF8\r
  79          * \r
  80          * @param inputFile\r
  81          *            the file containing the list of FASTA formatted sequences to\r
  82          *            read from\r
  83          * @throws FileNotFoundException\r
  84          *             if the input file is not found\r
  85          * @throws IllegalStateException\r
  86          *             if the close method was called on this instance\r
  87          * \r
  88          */\r
  89         public FastaReader(final String inputFile) throws FileNotFoundException {\r
  90                 input = new Scanner(new File(inputFile), "UTF8");\r
  91                 input.useDelimiter(DELIM);\r
  92                 Runtime.getRuntime().addShutdownHook(new Thread() {\r
  93 \r
  94                         @Override\r
  95                         public void run() {\r
  96                                 if (input != null) {\r
  97                                         input.close();\r
  98                                 }\r
  99                         }\r
 100                 });\r
 101         }\r
 102 \r
 103         /**\r
 104          * This class will not close the incoming stream! So the client should do\r
 105          * so.\r
 106          * \r
 107          * @param inputStream\r
 108          * @throws FileNotFoundException\r
 109          */\r
 110         public FastaReader(final InputStream inputStream)\r
 111                         throws FileNotFoundException {\r
 112                 input = new Scanner(inputStream);\r
 113                 input.useDelimiter(DELIM);\r
 114         }\r
 115         /**\r
 116          * {@inheritDoc}\r
 117          * \r
 118          * @throws IllegalStateException\r
 119          *             if the close method was called on this instance\r
 120          */\r
 121         @Override\r
 122         public boolean hasNext() {\r
 123                 return input.hasNext();\r
 124         }\r
 125 \r
 126         /**\r
 127          * Reads the next FastaSequence from the input\r
 128          * \r
 129          * @throws AssertionError\r
 130          *             if the header or the sequence is missing\r
 131          * @throws IllegalStateException\r
 132          *             if the close method was called on this instance\r
 133          *             @throws MismatchException - if there were no more FastaSequence's.\r
 134          */\r
 135         @Override\r
 136         public FastaSequence next() {\r
 137                 String fastaHeader=input.next();\r
 138                 while (fastaHeader.indexOf("\n")<0 && input.hasNext())\r
 139                 {\r
 140                         fastaHeader = fastaHeader.concat(">");\r
 141                         fastaHeader = fastaHeader.concat(input.next());\r
 142                 }\r
 143                 return FastaReader.toFastaSequence(fastaHeader);\r
 144         }\r
 145 \r
 146         /**\r
 147          * Not implemented\r
 148          */\r
 149         @Override\r
 150         public void remove() {\r
 151                 throw new UnsupportedOperationException();\r
 152         }\r
 153 \r
 154         /**\r
 155          * Call this method to close the connection to the input file if you want to\r
 156          * free up the resources. The connection will be closed on the JVM shutdown\r
 157          * if this method was not called explicitly. No further reading on this\r
 158          * instance of the FastaReader will be possible after calling this method.\r
 159          */\r
 160         public void close() {\r
 161                 input.close();\r
 162         }\r
 163 \r
 164         private static FastaSequence toFastaSequence(final String singleFastaEntry) {\r
 165 \r
 166                 assert !Util.isEmpty(singleFastaEntry) : "Empty String where FASTA sequence is expected!";\r
 167 \r
 168                 int nlineidx = singleFastaEntry.indexOf("\n");\r
 169                 if (nlineidx < 0) {\r
 170                         throw new AssertionError(\r
 171                                         "The FASTA sequence must contain the header information"\r
 172                                                         + " separated by the new line from the sequence. Given sequence does not appear to "\r
 173                                                         + "contain the header! Given data:\n "\r
 174                                                         + singleFastaEntry);\r
 175                 }\r
 176                 String header = singleFastaEntry.substring(0, nlineidx);\r
 177 \r
 178                 // Get rid of the new line chars (should cover common cases)\r
 179                 header = header.replaceAll("\r", "");\r
 180 \r
 181                 String sequence = singleFastaEntry.substring(nlineidx);\r
 182 \r
 183                 if (Util.isEmpty(sequence)) {\r
 184                         throw new AssertionError(\r
 185                                         "Empty sequences are not allowed! Please make sure the "\r
 186                                                         + " data is in the FASTA format! Given data:\n "\r
 187                                                         + singleFastaEntry);\r
 188                 }\r
 189                 return new FastaSequence(header, sequence);\r
 190         }\r
 191 }\r