Bio::SeqIO::fastq(3)

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

SYNOPSIS
Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION
This object can transform Bio::Seq and Bio::Seq::SeqWithQuality objects to and from fastq flat file databases.

Fastq is a file format used frequently at the Sanger Centre to bundle a fasta sequence and its quality data. A typical fastaq entry takes the from:

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

Fastq files have sequence and quality data on a single line and the quality values are single-byte encoded. To retrieve the decimal values for qualities you need to subtract 33 (or Octal 41) from each byte and then convert to a '2 digit + 1 space' integer. You can check if 33 is the right number because the first byte which is always '!' corresponds to a quality value of 0.

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/MailList.shtml - About the mailing lists

  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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/

AUTHORS - Tony Cox
Email: avc@sanger.ac.uk

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

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

  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::SeqWithQuality or Bio::seq object

  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::SeqWithQuality object

  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::SeqWithQuality object