- AUTHOR Chad Matsalla
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
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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::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.
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.
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?)
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