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

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)

perl v5.32.1			  2019-12-07		  Bio::SeqIO::fastq(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHORS - Chris Fields (taken over from Tony Cox) | APPENDIX | Bio::SeqIO interface methods | Plugin-specific methods

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