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Итак, я пишу этот код, который будет считывать файл fasta. В файле fasta будет 10 последовательностей. Начало последовательности будет «>» Я хочу разделить 50: 50 этих последовательностей и создать с ним два новых файла fasta. 5 последовательностей в одном новом файле; остальные 5 последовательностей в другом новом файле.

У меня есть интерфейс, который является самой последовательностью, и класс файлов fasta с 10 последовательностями реализует его. У меня есть два класса для первых 5 последовательностей и последних 5 последовательностей. У меня есть программа чтения, которая считывает файл fasta. Я просто не знаю, как написать что-то, что разделит его на два файла. Должен ли я добавить другой класс, который разделяет, а затем другой, который создает? Я не уверен, как это сделать. пожалуйста, помогите ty

Пример формата файла fasta:

 >XP_012508841.1 PREDICTED: apolipoprotein E [Propithecus coquereli]
---------------------------MNALWAVVVVTFLAGCQAKVEPALE------LE
AGELTEWQTGQPWEQALGRFWDYLRWVQTLSNQVQEELLSSQVTQELTVLMEETMKEVKA
YKLELEEQMSPMAEETRARLSKELQAAQARLGQDMQDLRGRLEQYCSEAQAVLGQNTEEL
RARLAAHLRKLRKRLLRDAEDLQKRLAVYQAGAREGAERGVSAIRERLRPLVERGRTRAA
TVG-TLASQPLRERAQAWGERLRAGLEEMGARGRDRLDEVREQLEEVRAKVEEQAAQLRL
QAEAFESRLKSWFTPLVEDMQRQWAGLVEKLQAAVQSPTATPEPSTNH

>XP_012616817.1 apolipoprotein E [Microcebus murinus]
---------------------------MNALWAVVVVTFLAGCQAKVEPALE------PE
ARELTEWQTGQPWEQALGRFWDYLRWVQTLSDQVQEELLSSQVTQELTVLMEETMKELKA
YKSELEQQLNPMAEETRARLSKELQAAQARLGQDMQDLRGRLAQYRGEVQAMLGQSTDEL
RARFASHLRKLRKRLLRDAEDLQRRLAVYQAGAREGAERGVSAIRERLGPLVEQGRLRAA
TVG-TLAGQPLRERAEAWGERLRARLEEMGSQGRDRLDEVREQVEEVRVKVEEQAAKMRL
QAEALEARLKSWFTPLVEDMQRQWAGLVEKLQAAVQGTTATPEATENH

>XP_008047463.1 apolipoprotein E [Carlito syrichta]
---------------------------MKVLWAVLLVTFLAGGRADVEPELE------TE
LRKPAEWQSGQPWEAALGRLWDYLRWVQTLSDEVQEELLSSQVTQELT------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------
 

Изначально я создал метод (функцию) для синтаксического анализа последовательностей из файла Fasta, но, как и многие другие вещи, файлы Fasta могут быть в таком количестве форматов, что потребуется выполнить некоторую настройку, чтобы отличить один тип от другого типа. Ваши файлы Fasta не являются исключением, поскольку в большинстве последовательностей Fasta я не верю, что символ дефиса или минуса ( - ) разрешен в последовательности, если он не содержится в заголовке последовательности, но я вижу, что в ваших файлах Fasta дефисы содержатся в последовательностях. Конечно, я, скорее всего, ошибаюсь в этом. 😉

Теперь, когда это стало известно, я добавил некоторые дополнительные переменные, которые можно установить вручную, чтобы обеспечить большую гибкость в отношении различных форматов файлов Fasta (я надеюсь). На самом деле это должен быть класс, а не метод с самого начала, но я собираюсь позволить вам преобразовать его в работоспособный класс самостоятельно.

Это большой метод (и мне это не нравится) с большим количеством комментариев, но я хотел дать вам что-то относительно быстрое. Я рекомендую вам прочитать все предоставленные комментарии в коде.

После того, как вы попробуете это method…do сделайте из этого класс:

 /**
 * Returns a {@code List<String>} Interface object of all the Sequence Clusters 
 * detected within the supplied Fasta Data File.<br>
 * 
 * @param sourceFilePath (String) The full path and file name to the source 
 * Fasta data file to parse.<br>
 * 
 * @param destinationFileFolderPath (String)  The full path to the
 * destination directory (folder) where the two split Fasta files are to be 
 * created. If null or Null String ("") is supplied then the two split Fasta 
 * files will be created within the source file directory. Destination split 
 * file names are auto-generated!<br>
 * 
 * @param splitRatio (String) The ratio of sequence clusters to be applied to 
 * each created split Fasta files. Ratio is considered percentages and the 
 * highest percentage is first followed by the lower percentage delimited with 
 * a colon (:), for example: "60:40". The two values provided <b>must</b> sum 
 * to 100.<br>
 * 
 * @param newSequenceDesignator (String) By default an inner blank line is 
 * considered the end of a sequence cluster and the possible start of a new 
 * one. If a designator is supplied here then blank lines are ignored within 
 * the source file while parsing (if they exist). If there are no blank lines 
 * within the source file separating the sequence clusters then a designator 
 * <b>must</b> be supplied, usually the Sequence Cluster Header designator (>) 
 * is used. The New Sequence Designator can be the same as the Sequence Cluster 
 * Header Designator.<br>
 * 
 * @return ({@code List<String>}) The List of parsed Sequence Clusters from 
 * the supplied source Fasta data file.
 */
public static java.util.List<String> splitFastaFile(String sourceFilePath, String destinationFileFolderPath, 
                                 String splitRatio, String newSequenceDesignator) {
    /* System newline character(s) to use for console 
       display when required.   */
    String ls = System.lineSeparator();
    
    // Valid characters allowed to be contained within a Fasta sequence line.
    String allowableCharactersInSequences = "ABCDEFGHIJKLMNOPQRSTUVWXYZ-*";
    
    /* By default, any sequence cluster line (other than the Header) which 
       contains an invalid character (a character not stipulated within the
       'allowableCharactersInSequences' variable) is ignored and not added 
       to the Sequence Cluster. If however, you provide a string character 
       or phrase to the 'replaceInvalidSequenceCharactersWith' variable then 
       all invalid characters will be replace by what is held within that
       variable. Keep in mind that you should use a character or case phrase 
       that is not considered valid (where as it is not also contained within  
       the 'allowableCharactersInSequences' variable). You want to always 
       maintain an invalid sequence line as INVALID unless the replacement is 
       indeed a VALID responce (repair) to the sequence which makes up the 
       sequence line or Sequence Cluster.             */
    String replaceInvalidSequenceCharactersWith = null;     // Default is null.
    
    /* The String or string character that will denote 
       the start of a new Sequence cluster.  */
    String sequenceDesignatorString = ">";
    
    /* The String or string character that will denote
       the start of a Sequence Header line. Can be the 
       same as the Sequence Designator String.   */
    String sequenceHeaderDesignatorString = ">";
    
    // Escape RegEx meta characters in allowableCharactersInSequences (if any).
    allowableCharactersInSequences = allowableCharactersInSequences.replaceAll("[\W]", "\\$0");
    
    // Add the sequence Header (if any)
    boolean keepSequenceHeader = true;
    
    // Add a blank line between sequence clusters in created Split Fasta files.
    boolean blankLineBetweenSequenceClusters = false;
    
    /* If a comment is supplied to this variable then it MUST start with a 
       semicolon (;). If it doesn't then it will be nulled. This comment 
       will be applied as the fist line of any Split File created. The comment 
       provided can utilize one or all three of the method tags available.
       These tags are:        
            %H      The High percentabe Fasta sequences split value.
            %L      The Low percentabe Fasta sequences split value.
            %SV     The Split Value currently being processed.   
            %SFN    The Source File Name
    
       An example might be as what was provided below:     */
    String splitFileComment = ";SPLIT FASTA FILE - Source File: %SFN - Percent of source: %SV%";
    
    // See if the supplied source Fasta file exists.
    File f = new File(sourceFilePath);
    if (!f.exists() || !f.canRead()) {
        System.err.println("splitFastaFile() method error! Either the "
                  "specified source file can not be found or permission "
                  "to read the file does not exist!");
        return null;
    }
    
    /* Get the supplied Fasta file name. The destination
       files will derive from this name.        */
    String sourceFileName = f.getName();

    /* If null or null string ("") is passed as the destination 
       directory then the Source file directory will also become 
       the destination for the two created Split Files.         */  
    if (destinationFileFolderPath == null || destinationFileFolderPath.isEmpty()) {
        String absPath = new File(sourceFilePath).getAbsolutePath();
        destinationFileFolderPath = absPath.substring(0, absPath.lastIndexOf(File.separator));
    }
    
    /* Make sure the supplied destination file folder path
       contains a system file separator character ( or /).   */
    if (!destinationFileFolderPath.endsWith(File.separator)) {
        destinationFileFolderPath = destinationFileFolderPath   File.separator;
    }

    /* Make sure a proper Split Ratio is supplied! The Split Ratio is
       supplied as a colon (:) delimited string containg the desired 
       percentage of sequences to be saved within the first text file
       and the desired percentage of sequences to be saved to the second
       text file. If you want 80% of the sequences within the Fasta source
       file to be written to the first text file and you want the remaining
       20% to be written to the second text file then you would supply to
       the 'splitRatio' parameter:  "80:20". Whatever is supplied, the sum
       of the two supplied values MUST equal 100 (100%). The higher of the 
       two values MUST be first (this is enforced).              */
    if (!splitRatio.matches("\d{1,3}:\d{1,3}")) {
        System.err.println("splitFastaFile() method Error! An invalid Split "
                  "Ratio string was supplied! ("   splitRatio   ") The format "
                  "must be: "80:20".");
        return null;
    }
    /* Split the ratio string provided within the 'splitRatio' parameter.
       Convert the string numerical values to Integer and check validity. */
    String[] ratioParts = splitRatio.split("\s*:\s*");
    int high = Integer.valueOf(ratioParts[0]);
    int low = Integer.valueOf(ratioParts[1]);
    if (high   low != 100) {
        System.err.println("splitFastaFile() method Error! An invalid Split "
                  "Ratio string was supplied! ("   splitRatio   ") The percentage "
                  "values supplied must sum to 100. What was supplied sums to: "
                  (high   low)   ".");
        return null;
    }
    else if (high < low) {
        System.err.println("splitFastaFile() method Error! An invalid Split "
                  "Ratio string was supplied! ("   splitRatio   ") The higher "
                  "percentage value must be on the left and the lower percentage "
                  "value on the right! Swapping values to make it valid (" 
                  low   ":"   high   ")!");
        int tmp = high; 
        high = low; 
        low = tmp;
    }

    // Load source file Sequences into a List Interface object.
    List<String> sequenceList = new ArrayList<>();
    int fileLineCount = 0;
    int validDataLineCount = 0;
    int clusterLineCount = 0;
    try (BufferedReader reader = new BufferedReader(new FileReader(sourceFilePath))) {
        StringBuilder sb = new StringBuilder("");
        String line;
        while((line = reader.readLine()) != null) {
            /* Increment the File Lines Count (tracks the 
               total number of lines in Fasta source file). */
            fileLineCount  ;
            /* Trim off leading and trailing whitespaces, tabs, 
               etc from the read in data file line.   */
            line = line.trim();
            // Ignore lines that START with a simicolon (;). They are considered comment lines.
            if (line.startsWith(";")) { continue; }
            // Ignore first line of file if it's blank.
            if (line.isEmpty() amp;amp; validDataLineCount == 0) { continue; }
            // See if this is a Sequence Header Line and whether or not we are to keep it.
            if (line.startsWith(sequenceHeaderDesignatorString) amp;amp; !keepSequenceHeader) { 
                // Increment the Sequence Cluster Line Count.
                clusterLineCount  ;
                continue; // Ignore this Header...loop again.
            }
            if (validDataLineCount > 0 amp;amp; ((sequenceDesignatorString != null amp;amp; !sequenceDesignatorString.isEmpty()) ? line.startsWith(sequenceDesignatorString) : line.isEmpty())) {
                String tmpLine = "";
                if (line.startsWith(sequenceDesignatorString)) { 
                    tmpLine = line; 
                }
                sequenceList.add(sb.toString());
                sb.delete(0, sb.length());
                clusterLineCount = 0;
                if (!tmpLine.isEmpty()) {
                    sb.append(tmpLine).append(ls);
                    clusterLineCount  ;
                    validDataLineCount  ;
                }
            }
            else {
                /* Skip blank lines if it is set to not be the new Sequence designator.
                   By default, blank inner file lines are considered the designator for
                   the end of a Sequence Cluster and the beginning of a new one. if 
                   however the sequenceDesignatorString variable contains a designator 
                   then blank lines will be ignored.                    */
                if ((sequenceDesignatorString != null amp;amp; !sequenceDesignatorString.isEmpty()) amp;amp; line.isEmpty()) {
                    continue;
                }
                // Check sequence line validity
                else if (!line.startsWith(sequenceHeaderDesignatorString) amp;amp; !line.matches("["   allowableCharactersInSequences   "] ")) {
                    // NOT VALID!
                    // Do invalid Characters get replaced...
                    if (replaceInvalidSequenceCharactersWith != null amp;amp; 
                                    !replaceInvalidSequenceCharactersWith.isEmpty()) {
                        StringBuilder tmpSB = new StringBuilder("");
                        for (int i = 0; i < line.length(); i  ) {
                            String s = line.substring(i, i   1);
                            if (s.matches("["   allowableCharactersInSequences   "] ")) {
                                tmpSB.append(s);
                            }
                            else {
                                tmpSB.append(replaceInvalidSequenceCharactersWith);
                            }
                        }
                        clusterLineCount  ;
                        sb.append(tmpSB.toString()).append(ls);
                        validDataLineCount  ;
                        continue;
                    }
                    // Display the Invalid sequence line detected in console and...
                    System.err.println("Invalid sequence line character(s) detected in line #"   clusterLineCount   " of sequence cluster #"   (sequenceList.size()   1)   ", on file "
                              "line #"   fileLineCount   "!"   ls   line);
                    // point out the characters that are invalid with Caret (^)
                    // characters under the invalid file line.
                    for (int i = 0; i < line.length(); i  ) {
                        System.out.print(!line.substring(i, i   1)
                                .matches("["   allowableCharactersInSequences   "] ") ? "^" : " ");
                    }
                    System.out.println();
                }
                else {
                    clusterLineCount  ;
                    sb.append(line).append(ls);
                    validDataLineCount  ;
                }
            }
        }
        if (!sb.toString().isEmpty()) {
            sequenceList.add(sb.toString());
        }
    } catch (FileNotFoundException ex) {
        System.err.println(ex);
        return null;
    } catch (IOException ex) {
        System.err.println(ex);
        return null;
    }

    // Below is used for testing the method code...
    //System.out.println("There are "   sequenceList.size()   " sequence(s) within the source file.");
    //for (String str : sequenceList) {
    //    System.out.println(str);
    //}

    /* Auto-Generate destination file names. Destination file names will be in
       the format of:
                      "Split_{source File Name}_{High Percentage}.txt"
            and       "Split_{source File Name}_{Low Percentage}.txt"

       If the source file name is: "FastaFile010.txt" and the Split Ratio 
       supplied is: "60:40"  then the destination file names will be:
                      "Split_FastaFile010_60.txt"
            and       "Split_FastaFile010_40.txt"
    */
    String name = sourceFileName.substring(0, sourceFileName.lastIndexOf("."));
    String extension = sourceFileName.substring(sourceFileName.lastIndexOf("."));
    String highFileName = "Split_"   name   "_"   String.valueOf(high)   extension;
    String lowFileName = "Split_"   name   "_"   String.valueOf(low)   extension;

    //System.out.println(highFileName);  // For Testing...
    //System.out.println(lowFileName);   // For Testing...

    /* Determine the number of sequences for each file
       based on the number sequences contained within
       the Sequence List and the supplied desired Ratio. */
    int highSeqs = (int)((sequenceList.size() * high) * 0.01d);
    int lowSeqs = sequenceList.size() - highSeqs;
    
    // System.out.println(highSeqs   " | "   lowSeqs);     // For Testing...

    // Create the two Split Files based on the desired ratio...
    int c = 0;
    String destPath;
    int alreadyWritten = 0;
    // Loop to write create or overwrite two seperate text files.
    while (c < 2) {
        destPath = destinationFileFolderPath   (c == 0 ? highFileName : lowFileName);
        String uFormat = "UTF-8";       // Save text files in UTF-8 format.
        try {
            FileOutputStream outputStream = new FileOutputStream(destPath);
            OutputStreamWriter outputStreamWriter = new OutputStreamWriter(outputStream, uFormat);
            try (BufferedWriter bufferedWriter = new BufferedWriter(outputStreamWriter)) {
                // Apply a comment (if there is one) to the start of the current Split File.
                if (splitFileComment != null amp;amp; !splitFileComment.isEmpty()) {
                    // Replace method tags (if any - %H, %L, %SV):
                    String actFileComment = splitFileComment.trim()
                                            .replace("%H", String.valueOf(high))
                                            .replace("%L", String.valueOf(low))
                                            .replace("%SV", (c == 0 ? String.valueOf(high) : String.valueOf(low)))
                                            .replace("%SFN", sourceFileName);
                    bufferedWriter.write(actFileComment);
                    bufferedWriter.write(System.lineSeparator());
                }
                int i;
                for (i = alreadyWritten; i < sequenceList.size(); i  ) {
                    bufferedWriter.write(sequenceList.get(i));
                    /* Add a blank line after a sequence cluster is written to 
                       file in preparation for the next sequence but don't do 
                       this if it's the last sequence in the required set to be 
                       written. If you don't want a blank line between all your 
                       sequence clusters in the saved files then supply false to 
                       the 'blankLineBetweenSequenceClusters' variable.    */
                    if (blankLineBetweenSequenceClusters amp;amp; 
                            (i   1 - alreadyWritten) != (c == 0 ? highSeqs : lowSeqs)) {
                        bufferedWriter.write(System.lineSeparator());
                    }
                    // Write everything in buffer to file right away.
                    bufferedWriter.flush();
                    /* Stop writing to the first file is we've reach our
                       sequence limit for this file. Break out of the loop
                       so that file #2 can be written.           */
                    if (c == 0 amp;amp; (i   1) == highSeqs) { break; }
                }
                // Update how many sequences we've already written to files.
                alreadyWritten = i 1;
                // Close the current writter.
                bufferedWriter.close();
            }
        }
        catch (IOException e) {
            System.err.println(e);
            break;
        }
        /* Increment for which file we are currently writing to:
           0 = file #1 and 1 = file #2.         */
        c  ;
    }
    return sequenceList;
}
 

Пример использования:

 List<String> seqs = splitFastaFile("MyFastaFile.txt", null, "60:40", null);
if (seqs.size() > 0) {
    System.out.println("There were "   seqs.size()   " Sequence Clusters within the Fasta source file!");
}
else {
    System.err.println("There was Error while processing the supplied Fasta File!");
}