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 \r
  26 import compbio.util.Util;\r
  27 \r
  28 /**\r
  29  * Reads files with FASTA formatted sequences. All the information in the FASTA\r
  30  * header is preserved including trailing white spaces. All the white spaces are\r
  31  * removed from the sequence.\r
  32  * \r
  33  * Examples of the correct input:\r
  34  * \r
  35  * <pre>\r
  36  * \r
  37  * >zedpshvyzg\r
  38  * GCQDKNNIAELNEIMGTTRSPSDWQHMKGASPRAEIGLTGKKDSWWRHCCSKEFNKTPPPIHPDMKRWGWMWNRENFEKFLIDNFLNPPCPRLMLTKGTWWRHEDLCHEIFWSTLRWLCLGNQSFSAMIWGHLCECHRMIWWESNEHMFWLKFRRALKKMNSNGPCMGPDNREWMITNRMGKEFCGPAFAGDCQSCWRKCHKTNKICFNEKKGTPTKIDHEQKDIMDILKDIDNHRNWKQCQLWLLTSKSTDQESTTMLTWSTWRDFFIIIKQPFDHKCRGALDANGDFQIAAELKWPAPMIILRQNQKTMHDKSCHHFFTNRCPLMHTTRANDKQCSWHTRKQFICQQDFTTWQHRPDTHRILPSWCMSTRRKNHIKNTPALAFSTCEMGDLPNGWAPGTIILQRQFTQAIKLPQETTGWPRCDPKFDHWNMSKWLRQLLGRDDEMIPPQCD\r
  39  * \r
  40  * >xovkactesa\r
  41  * CPLSKWWNRRAFLSHTANHWMILMTWEGPHDGESKMRIAMMKWSPCKPTMSHFRCGLDAWAEPIRQIACESTFRM\r
  42  * FCTTPRPIHKLTEMWGHMNGWTGAFCRQLECEWMMPPRHPHPCTSTFNNNKKRLIGQIPNEGKQLFINFQKPQHG\r
  43  * FSESDIWIWKDNPTAWHEGLTIAGIGDGQHCWNWMPMPWSGAPTSNALIEFWTWLGMIGTRCKTQGMWWDAMNHH\r
  44  * DQFELSANAHIAAHHMEKKMILKPDDRNLGDDTWMPPGKIWMRMFAKNTNACWPEGCRDDNEEDDCGTHNLHRMC\r
  45  * \r
  46  * >ntazzewyvv\r
  47  * CGCKIF D D NMKDNNRHG TDIKKHGFMH IRHPE KRDDC FDNHCIMPKHRRWGLWD\r
  48  * EASINM       AQQWRSLPPSRIMKLNG       HGCDCMHSHMEAD   DTKQSGIKGTFWNG  HDAQWLCRWG      \r
  49  * EFITEA       WWGRWGAITFFHAH  ENKNEIQECSDQNLKE        SRTTCEIID   TCHLFTRHLDGW \r
  50  *   RCEKCQANATHMTW ACTKSCAEQW  FCAKELMMN    \r
  51  *   W        KQMGWRCKIFRKLFRDNCWID  FELPWWPICFCCKGLSTKSHSAHDGDQCRRW    WPDCARDWLGPGIRGEF   \r
  52  *   FCTHICQQLQRNFWCGCFRWNIEKRMFEIFDDNMAAHWKKCMHFKFLIRIHRHGPITMKMTWCRSGCCFGKTRRLPDSSFISAFLDPKHHRDGSGMMMWSSEMRSCAIPDPQQAWNQGKWIGQIKDWNICFAWPIRENQQCWATPHEMPSGFHFILEKWDALAHPHMHIRQKKCWAWAFLSLMSSTHSDMATFQWAIPGHNIWSNWDNIICGWPRI\r
  53  * \r
  54  *    > 12 d t y wi             k       jbke    \r
  55  *   KLSHHDCD\r
  56  *    N\r
  57  *     H\r
  58  *     HSKCTEPHCGNSHQMLHRDP\r
  59  *     CCDQCQSWEAENWCASMRKAILF\r
  60  * \r
  61  * </pre>\r
  62  * \r
  63  * @author Peter Troshin\r
  64  * @version 1.0 April 2011\r
  65  * \r
  66  */\r
  67 public class FastaReader implements Iterator<FastaSequence> {\r
  68 \r
  69         private final Scanner input;\r
  70 \r
  71         /**\r
  72          * Header data can contain non-ASCII symbols and read in UTF8\r
  73          * \r
  74          * @param input\r
  75          *            the file containing the list of FASTA formatted sequences to\r
  76          *            read from\r
  77          * @throws FileNotFoundException\r
  78          *             if the input file is not found\r
  79          * @throws IllegalStateException\r
  80          *             if the close method was called on this instance\r
  81          * \r
  82          */\r
  83         public FastaReader(final String inputFile) throws FileNotFoundException {\r
  84                 input = new Scanner(new File(inputFile), "UTF8");\r
  85                 input.useDelimiter("\\s*>");\r
  86                 Runtime.getRuntime().addShutdownHook(new Thread() {\r
  87 \r
  88                         @Override\r
  89                         public void run() {\r
  90                                 if (input != null) {\r
  91                                         input.close();\r
  92                                 }\r
  93                         }\r
  94                 });\r
  95         }\r
  96 \r
  97         /**\r
  98          * This class will not close the incoming stream! So the client should do\r
  99          * so.\r
 100          * \r
 101          * @param inputStream\r
 102          * @throws FileNotFoundException\r
 103          */\r
 104         public FastaReader(final InputStream inputStream)\r
 105                         throws FileNotFoundException {\r
 106                 input = new Scanner(inputStream);\r
 107                 input.useDelimiter("\\s*>");\r
 108         }\r
 109         /**\r
 110          * {@inheritDoc}\r
 111          * \r
 112          * @throws IllegalStateException\r
 113          *             if the close method was called on this instance\r
 114          */\r
 115         @Override\r
 116         public boolean hasNext() {\r
 117                 return input.hasNext();\r
 118         }\r
 119 \r
 120         /**\r
 121          * Reads the next FastaSequence from the input\r
 122          * \r
 123          * @throws AssertionError\r
 124          *             if the header or the sequence is missing\r
 125          * @throws IllegalStateException\r
 126          *             if the close method was called on this instance\r
 127          */\r
 128         @Override\r
 129         public FastaSequence next() {\r
 130                 return FastaReader.toFastaSequence(input.next());\r
 131         }\r
 132 \r
 133         /**\r
 134          * Not implemented\r
 135          */\r
 136         @Override\r
 137         public void remove() {\r
 138                 throw new UnsupportedOperationException();\r
 139         }\r
 140 \r
 141         /**\r
 142          * Call this method to close the connection to the input file if you want to\r
 143          * free up the resources. The connection will be closed on the JVM shutdown\r
 144          * if this method was not called explicitly. No further reading on this\r
 145          * instance of the FastaReader will be possible after calling this method.\r
 146          */\r
 147         public void close() {\r
 148                 input.close();\r
 149         }\r
 150 \r
 151         private static FastaSequence toFastaSequence(final String singleFastaEntry) {\r
 152 \r
 153                 assert !Util.isEmpty(singleFastaEntry) : "Empty String where FASTA sequence is expected!";\r
 154 \r
 155                 int nlineidx = singleFastaEntry.indexOf("\n");\r
 156                 if (nlineidx < 0) {\r
 157                         throw new AssertionError(\r
 158                                         "The FASTA sequence must contain the header information"\r
 159                                                         + " separated by the new line from the sequence. Given sequence does not appear to "\r
 160                                                         + "contain the header! Given data:\n "\r
 161                                                         + singleFastaEntry);\r
 162                 }\r
 163                 String header = singleFastaEntry.substring(0, nlineidx);\r
 164 \r
 165                 // Get rid of the new line chars (should cover common cases)\r
 166                 header = header.replaceAll("\r", "");\r
 167 \r
 168                 String sequence = singleFastaEntry.substring(nlineidx);\r
 169 \r
 170                 if (Util.isEmpty(sequence)) {\r
 171                         throw new AssertionError(\r
 172                                         "Empty sequences are not allowed! Please make sure the "\r
 173                                                         + " data is in the FASTA format! Given data:\n "\r
 174                                                         + singleFastaEntry);\r
 175                 }\r
 176                 return new FastaSequence(header, sequence);\r
 177         }\r
 178 }\r