Sendu Bala
and 1 contributors


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


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


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


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AUTHOR Chad Matsalla

Chad Matsalla


Jason Stajich,


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


 Title   : next_seq()
 Usage   : $swq = $stream->next_seq()
 Function: returns the next phred sequence in the stream
 Returns : Bio::Seq::Quality 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.


 Title   : write_seq(-Quality => $swq, <comments>)
 Usage   : $obj->write_seq(     -Quality => $swq,);
 Function: Write out an scf.
 Returns : Nothing.
 Args    : Requires: a reference to a Quality 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()
        PHRED_VERSION: 0.980904.e
        CALL_METHOD: phred
        QUALITY_LEVELS: 99
        TIME: <current time>
        TRACE_ARRAY_MAX_INDEX: unknown
        CHEM: unknown
        DYE: unknown
     IMPORTANT: This method does not write the trace index where this
          call was made. All base calls are placed at index 1.