Bio::SeqIO::fastq.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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 from:

   @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
 
 

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:
   http://bugzilla.open-bio.org/
 
 

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)