Bio::SeqIO::fastq(3pm)					User Contributed Perl Documentation				    Bio::SeqIO::fastq(3pm)

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://redmine.open-bio.org/projects/bioperl/

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'   (orginal 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)

perl v5.14.2							    2012-03-02						    Bio::SeqIO::fastq(3pm)