Ewan Birney

NAME

Bio::SeqIO::phd - .phd file input/output stream

SYNOPSIS

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

DESCRIPTION

This object can transform .phd files (from Phil Green's phred basecaller) to and from Bio::Seq::SeqWithQuality objects

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://www.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://bio.perl.org/bioperl-bugs/

AUTHOR Chad Matsalla

Chad Matsalla bioinformatics@dieselwurks.com

CONTRIBUTORS

Jason Stajich, jason@bioperl.org

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   : $swq = $stream->next_seq()
 Function: returns the next phred sequence in the stream
 Returns : Bio::Seq::SeqWithQuality object
 Args    : NONE
 Notes   : This is really redundant because AFAIK there is no such thing as
           a .phd file that contains more then one sequence. It is included as
           an interface thing and for consistency.

_next_phd()

 Title   : _next_phd()
 Usage   : $seq = $stream->_next_phd() (but do not do this. use next_seq()
        instead.)
 Function: returns the next phred sequence in the stream
 Returns : Bio::Seq::SeqWithQuality object
 Args    : NONE
 Notes   : An internal method. Use next_seq.

next_primary_phd()

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

write_seq

 Title   : write_seq(-SeqWithQuality => $swq, <comments>)
 Usage   : $obj->write_seq(     -SeqWithQuality => $swq,);
 Function: Write out an scf.
 Returns : Nothing.
 Args    : Requires: a reference to a SeqWithQuality object to form the
           basis for the scf. Any other arguments are assumed to be comments
           and are put into the comments section of the scf. Read the
           specifications for scf to decide what might be good to put in here.
 Notes   : These are the comments that reside in the header of a phd file
           at the present time. If not provided in the parameter list for
           write_phd(), the following default values will be used:
        CHROMAT_FILE: $swq->id()
        ABI_THUMBPRINT: 0
        PHRED_VERSION: 0.980904.e
        CALL_METHOD: phred
        QUALITY_LEVELS: 99
        TIME: <current time>
        TRACE_ARRAY_MIN_INDEX: 0
        TRACE_ARRAY_MAX_INDEX: unknown
        CHEM: unknown
        DYE: unknown