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Bio::SeqIO::phd.3pm

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::Quality 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://bioperl.org/wiki/Mailing_lists  - 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 the web:

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

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::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.
 
 

write_seq

  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()
         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
      IMPORTANT: This method does not write the trace index where this
           call was made. All base calls are placed at index 1.