Package org.biojava.bio.seq.io

Class SeqIOTools

  • public final class SeqIOTools
extends Object
    Deprecated.
    use org.biojavax.bio.seq.RichSequence.IOTools
    A set of convenience methods for handling common file formats.
    Since:
    1.1
    Author:
    Thomas Down, Mark Schreiber, Nimesh Singh, Matthew Pocock, Keith James

    • Method Detail

      • readEmbl

        public static SequenceIterator readEmbl​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an EMBL-format stream.
        Parameters:
        br - A reader for the EMBL source or file
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readEmblRNA

        public static SequenceIterator readEmblRNA​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an EMBL-format stream, but for RNA.
        Parameters:
        br - A reader for the EMBL source or file
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readEmblNucleotide

        public static SequenceIterator readEmblNucleotide​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an EMBL-format stream.
        Parameters:
        br - A reader for the EMBL source or file
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readGenbank

        public static SequenceIterator readGenbank​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an Genbank-format stream.
        Parameters:
        br - A reader for the Genbank source or file
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readGenbankXml

        public static SequenceIterator readGenbankXml​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an GenbankXML-format stream.
        Parameters:
        br - A reader for the GenbanXML source or file
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readGenpept

        public static SequenceIterator readGenpept​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an Genpept-format stream.
        Parameters:
        br - A reader for the Genpept source or file
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readSwissprot

        public static SequenceIterator readSwissprot​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an Swissprot-format stream.
        Parameters:
        br - A reader for the Swissprot source or file
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readFasta

        public static SequenceIterator readFasta​(BufferedReader br,
                                         SymbolTokenization sTok)
        Deprecated.
        Read a fasta file.
        Parameters:
        br - the BufferedReader to read data from
        sTok - a SymbolTokenization that understands the sequences
        Returns:
        a SequenceIterator over each sequence in the fasta file

      • readFasta

        public static SequenceIterator readFasta​(BufferedReader br,
                                         SymbolTokenization sTok,
                                         SequenceBuilderFactory seqFactory)
        Deprecated.
        Read a fasta file using a custom type of SymbolList. For example, use SmartSequenceBuilder.FACTORY to emulate readFasta(BufferedReader, SymbolTokenization) and SmartSequenceBuilder.BIT_PACKED to force all symbols to be encoded using bit-packing.
        Parameters:
        br - the BufferedReader to read data from
        sTok - a SymbolTokenization that understands the sequences
        seqFactory - a factory used to build a SymbolList
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readFastaDNA

        public static SequenceIterator readFastaDNA​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an FASTA-format stream of DNA sequences.
        Parameters:
        br - the BufferedReader to read data from
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readFastaRNA

        public static SequenceIterator readFastaRNA​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an FASTA-format stream of RNA sequences.
        Parameters:
        br - the BufferedReader to read data from
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readFastaProtein

        public static SequenceIterator readFastaProtein​(BufferedReader br)
        Deprecated.
        Iterate over the sequences in an FASTA-format stream of Protein sequences.
        Parameters:
        br - the BufferedReader to read data from
        Returns:
        a SequenceIterator that iterates over each Sequence in the file

      • readFasta

        public static SequenceDB readFasta​(InputStream seqFile,
                                   Alphabet alpha)
                            throws BioException
        Deprecated.
        Create a sequence database from a fasta file provided as an input stream. Note this somewhat duplicates functionality in the readFastaDNA and readFastaProtein methods but uses a stream rather than a reader and returns a SequenceDB rather than a SequenceIterator. If the returned DB is likely to be large then the above mentioned methods should be used.
        Parameters:
        seqFile - The file containg the fasta formatted sequences
        alpha - The Alphabet of the sequence, ie DNA, RNA etc
        Returns:
        a SequenceDB containing all the Sequences in the file.
        Throws:
        BioException - if problems occur during reading of the stream.
        Since:
        1.2

      • writeFasta

        public static void writeFasta​(OutputStream os,
                              SequenceDB db)
                       throws IOException
        Deprecated.
        Write a sequenceDB to an output stream in fasta format.
        Parameters:
        os - the stream to write the fasta formatted data to.
        db - the database of Sequences to write
        Throws:
        IOException - if there was an error while writing.
        Since:
        1.2

      • writeFasta

        public static void writeFasta​(OutputStream os,
                              SequenceIterator in)
                       throws IOException
        Deprecated.
        Writes sequences from a SequenceIterator to an OutputStream in Fasta Format. This makes for a useful format filter where a StreamReader can be sent to the StreamWriter after formatting.
        Parameters:
        os - The stream to write fasta formatted data to
        in - The source of input Sequences
        Throws:
        IOException - if there was an error while writing.
        Since:
        1.2

      • writeFasta

        public static void writeFasta​(OutputStream os,
                              Sequence seq)
                       throws IOException
        Deprecated.
        Writes a single Sequence to an OutputStream in Fasta format.
        Parameters:
        os - the OutputStream.
        seq - the Sequence.
        Throws:
        IOException - if there was an error while writing.

      • writeEmbl

        public static void writeEmbl​(OutputStream os,
                             SequenceIterator in)
                      throws IOException
        Deprecated.
        Writes a stream of Sequences to an OutputStream in EMBL format.
        Parameters:
        os - the OutputStream.
        in - a SequenceIterator.
        Throws:
        IOException - if there was an error while writing.

      • writeEmbl

        public static void writeEmbl​(OutputStream os,
                             Sequence seq)
                      throws IOException
        Deprecated.
        Writes a single Sequence to an OutputStream in EMBL format.
        Parameters:
        os - the OutputStream.
        seq - the Sequence.
        Throws:
        IOException - if there was an error while writing.

      • writeGenbank

        public static void writeGenbank​(OutputStream os,
                                Sequence seq)
                         throws IOException
        Deprecated.
        Writes a single Sequence to an OutputStream in Genbank format.
        Parameters:
        os - the OutputStream.
        seq - the Sequence.
        Throws:
        IOException - if there was an error while writing.

      • identifyFormat

        public static int identifyFormat​(String formatName,
                                 String alphabetName)
        Deprecated.
        identifyFormat performs a case-insensitive mapping of a pair of common sequence format name (such as 'embl', 'genbank' or 'fasta') and alphabet name (such as 'dna', 'rna', 'protein', 'aa') to an integer. The value returned will be one of the public static final fields in SeqIOConstants, or a bitwise-or combination of them. The method will reject known illegal combinations of format and alphabet (such as swissprot + dna) by throwing an IllegalArgumentException. It will return the SeqIOConstants.UNKNOWN value when either format or alphabet are unknown.
        Parameters:
        formatName - a String.
        alphabetName - a String.
        Returns:
        an int.

      • getSequenceFormat

        public static SequenceFormat getSequenceFormat​(int identifier)
                                        throws BioException
        Deprecated.
        getSequenceFormat accepts a value which represents a sequence format and returns the relevant SequenceFormat object.
        Parameters:
        identifier - an int which represents a binary value with bits set according to the scheme described in SeqIOConstants.
        Returns:
        a SequenceFormat.
        Throws:
        BioException - if an error occurs.

      • getBuilderFactory

        public static SequenceBuilderFactory getBuilderFactory​(int identifier)
                                                throws BioException
        Deprecated.
        getBuilderFactory accepts a value which represents a sequence format and returns the relevant SequenceBuilderFactory object.
        Parameters:
        identifier - an int which represents a binary value with bits set according to the scheme described in SeqIOConstants.
        Returns:
        a SequenceBuilderFactory.
        Throws:
        BioException - if an error occurs.

      • getAlphabet

        public static FiniteAlphabet getAlphabet​(int identifier)
                                  throws BioException
        Deprecated.
        getAlphabet accepts a value which represents a sequence format and returns the relevant FiniteAlphabet object.
        Parameters:
        identifier - an int which represents a binary value with bits set according to the scheme described in SeqIOConstants.
        Returns:
        a FiniteAlphabet.
        Throws:
        BioException - if an error occurs.

      • guessFileType

        public static int guessFileType​(File seqFile)
                         throws IOException,
                                FileNotFoundException
        Deprecated.
        because there is no standard file naming convention and guessing by file name is inherantly error prone and bad.
        Attempts to guess the filetype of a file given the name. For use with the functions below that take an int fileType as a parameter. EMBL and Genbank files are assumed to contain DNA sequence.
        Parameters:
        seqFile - the File to read from.
        Returns:
        a value that describes the file type.
        Throws:
        IOException - if seqFile cannot be read
        FileNotFoundException - if seqFile cannot be found

      • formatToFactory

        public static SequenceBuilderFactory formatToFactory​(SequenceFormat format,
                                                     Alphabet alpha)
                                              throws BioException
        Deprecated.
        as this essentially duplicates the operation available in the method identifyBuilderFactory.
        Attempts to retrieve the most appropriate SequenceBuilder object for some combination of Alphabet and SequenceFormat
        Parameters:
        format - currently supports FastaFormat, GenbankFormat, EmblLikeFormat
        alpha - currently only supports the DNA and Protein alphabets
        Returns:
        the SequenceBuilderFactory
        Throws:
        BioException - if the combination of alpha and format is unrecognized.

      • fileToBiojava

        public static Object fileToBiojava​(String formatName,
                                   String alphabetName,
                                   BufferedReader br)
                            throws BioException
        Deprecated.
        Reads a file with the specified format and alphabet
        Parameters:
        formatName - the name of the format eg genbank or swissprot (case insensitive)
        alphabetName - the name of the alphabet eg dna or rna or protein (case insensitive)
        br - a BufferedReader for the input
        Returns:
        either an Alignment object or a SequenceIterator (depending on the format read)
        Throws:
        BioException - if an error occurs while reading or a unrecognized format, alphabet combination is used (eg swissprot and DNA).
        Since:
        1.3

      • fileToBiojava

        public static Object fileToBiojava​(int fileType,
                                   BufferedReader br)
                            throws BioException
        Deprecated.
        Reads a file and returns the corresponding Biojava object. You need to cast it as an Alignment or a SequenceIterator as appropriate.
        Parameters:
        fileType - a value that describes the file type
        br - the reader for the input
        Returns:
        either a SequenceIterator if the file type is a sequence file, or a Alignment if the file is a sequence alignment.
        Throws:
        BioException - if the file cannot be parsed

      • biojavaToFile

        public static void biojavaToFile​(int fileType,
                                 OutputStream os,
                                 Object biojava)
                          throws BioException,
                                 IOException,
                                 IllegalSymbolException
        Deprecated.
        Converts a Biojava object to the given filetype.
        Parameters:
        fileType - a value that describes the type of sequence file
        os - the stream to write the formatted results to
        biojava - a SequenceIterator, SequenceDB, Sequence, or Alignment
        Throws:
        BioException - if biojava cannot be converted to that format.
        IOException - if the output cannot be written to os
        IllegalSymbolException - if biojava contains a Symbol that cannot be understood by the parser.