Provided by: libbio-perl-perl_1.7.8-1_all bug

NAME

       Bio::SeqIO::fastq - fastq sequence input/output stream

SYNOPSIS

         ################## pertains to FASTQ parsing only ##################

         # grabs the FASTQ parser, specifies the Illumina variant
         my $in = Bio::SeqIO->new(-format    => 'fastq-illumina',
                                  -file      => 'mydata.fq');

         # simple 'fastq' format defaults to 'sanger' variant
         my $out = Bio::SeqIO->new(-format    => 'fastq',
                                   -file      => '>mydata.fq');

         # $seq is a Bio::Seq::Quality object
         while (my $seq = $in->next_seq) {
             $out->write_seq($seq);  # convert Illumina 1.3 to Sanger format
         }

         # for 4x faster parsing, one can do something like this for raw data
         use Bio::Seq::Quality;

         # $data is a hash reference containing all arguments to be passed to
         # the Bio::Seq::Quality constructor
         while (my $data = $in->next_dataset) {
             # process $data, such as trim, etc
             my $seq = Bio::Seq::Quality->new(%$data);

             # for now, write_seq only accepts Bio::Seq::Quality, but may be modified
             # to allow raw hash references for speed
             $out->write_seq($data);
         }

DESCRIPTION

       This object can transform Bio::Seq and Bio::Seq::Quality objects to and from FASTQ flat
       file databases.

       FASTQ is a file format used frequently at the Sanger Centre and in next-gen sequencing to
       bundle a FASTA sequence and its quality data. A typical FASTQ entry takes the form:

         @HCDPQ1D0501
         GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT.....
         +HCDPQ1D0501
         !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65.....

       where:

         @ = descriptor, followed by one or more sequence lines
         + = optional descriptor (if present, must match first one), followed by one or
             more qual lines

       When writing FASTQ output the redundant descriptor following the '+' is by default left
       off to save disk space. If needed, one can set the quality_header() flag in order for this
       to be printed.

   FASTQ and Bio::Seq::Quality mapping
       FASTQ files have sequence and quality data on single line or multiple lines, and the
       quality values are single-byte encoded. Data are mapped very simply to Bio::Seq::Quality
       instances:

           Data                                        Bio::Seq::Quality method
           ------------------------------------------------------------------------
           first non-whitespace chars in descriptor    id^
           descriptor line                             desc^
           sequence lines                              seq
           quality                                     qual*
           FASTQ variant                               namespace

           ^ first nonwhitespace chars are id(), everything else after (to end of line)
             is in desc()
           * Converted to PHRED quality scores where applicable ('solexa')

   FASTQ variants
       This parser supports all variants of FASTQ, including Illumina v 1.0 and 1.3:

           variant                note
           -----------------------------------------------------------
           sanger                 original
           solexa                 Solexa, Inc. (2004), aka Illumina 1.0
           illumina               Illumina 1.3

       The variant can be specified by passing by either passing the additional -variant
       parameter to the constructor:

         my $in = Bio::SeqIO->new(-format    => 'fastq',
                                  -variant   => 'solexa',
                                  -file      => 'mysol.fq');

       or by passing the format and variant together (Bio::SeqIO will now handle this and convert
       it accordingly to the proper argument):

         my $in = Bio::SeqIO->new(-format    => 'fastq-solexa',
                                  -file      => 'mysol.fq');

       Variants can be converted back and forth from one another; however, due to the difference
       in scaling for solexa quality reads, converting from 'illumina' or 'sanger' FASTQ to
       solexa is not recommended.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to one of the Bioperl mailing lists.  Your
       participation is much appreciated.

         bioperl-l@bioperl.org                  - General discussion
         http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will
       be able look at the problem and quickly address it. Please include a thorough description
       of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their
       resolution.  Bug reports can be submitted via the web:

         https://github.com/bioperl/bioperl-live/issues

AUTHORS - Chris Fields (taken over from Tony Cox)

       Email: cjfields at bioperl dot org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are
       usually preceded with a _

Bio::SeqIO interface methods

   next_seq
        Title    : next_seq
        Usage    : $seq = $stream->next_seq()
        Function : returns the next sequence in the stream
        Returns  : Bio::Seq::Quality object
        Args     : NONE
        Status   : Stable

   write_seq
        Title    : write_seq
        Usage    : $stream->write_seq(@seq)
        Function : writes the $seq object into the stream
        Returns  : 1 for success and 0 for error
        Args     : Bio::Seq::Quality
        Note     : This now conforms to SeqIO spec (module output is same format as
                   next_seq)
        Status   : Stable

   variant
        Title   : variant
        Usage   : $format  = $obj->variant();
        Function: Get and set method for the quality sequence variant.  This is
                  important for indicating the encoding/decoding to be used for
                  quality data.

                  Current values accepted are:
                   'sanger'   (original FASTQ)
                       ASCII encoding from 33-126, PHRED quality score from 0 to 93
                   'solexa'   (aka illumina1.0)
                       ASCII encoding from 59-104, SOLEXA quality score from -5 to 40
                   'illumina' (aka illumina1.3)
                       ASCII encoding from 64-104, PHRED quality score from 0 to 40

                   (Derived from the MAQ website):
                   For 'solexa', scores are converted to PHRED qual scores using:
                       $Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10)

        Returns : string
        Args    : new value, string

Plugin-specific methods

   next_dataset
        Title    : next_dataset
        Usage    : $obj->next_dataset
        Function : returns a hash reference containing the parsed data
        Returns  : hash reference
        Args     : none
        Status   : Stable

   write_fastq
        Title   : write_fastq
        Usage   : $stream->write_fastq(@seq)
        Function: writes the $seq object into the stream
        Returns : 1 for success and 0 for error
        Args    : Bio::Seq::Quality object
        Status  : Deprecated (delegates to write_seq)

   write_fasta
        Title   : write_fasta
        Usage   : $stream->write_fasta(@seq)
        Function: writes the $seq object into the stream
        Returns : 1 for success and 0 for error
        Args    : Bio::Seq object
        Note    : This method does not currently delegate to Bio::SeqIO::fasta
                  (maybe it should?).  Not sure whether we should keep this as a
                  convenience method.
        Status  : Unstable

   write_qual
        Title   : write_qual
        Usage   : $stream->write_qual(@seq)
        Function: writes the $seq object into the stream
        Returns : 1 for success and 0 for error
        Args    : Bio::Seq::Quality object
        Note    : This method does not currently delegate to Bio::SeqIO::qual
                  (maybe it should?).  Not sure whether we should keep this as a
                  convenience method.
        Status  : Unstable

   validate
        Title    : validate
        Usage    : $obj->validate(0)
        Function : flag for format/qual range validation - default is 1, validate
        Returns  : Bool (0/1)
        Args     : Bool (0/1)
        Status   : Stable (may be moved to interface)

   quality_header
        Title    : quality_header
        Usage    : $obj->quality_header
        Function : flag for printing quality header - default is 0, no header
        Returns  : Bool (0/1)
        Args     : Bool (0/1)
        Status   : Unstable (name may change dep. on feedback)