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::SeqWithQuality objects

Mailing Lists
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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/ Chad Matsalla bioinformatics@dieselwurks.com Jason Stajich, jason@bioperl.org 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.

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