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