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NAMEBio::SeqIO::phd - phd file input/output stream SYNOPSISDo not use this module directly. Use it via the Bio::SeqIO class. DESCRIPTIONThis object can transform .phd files (from Phil Green's phred basecaller) to and from Bio::Seq::Quality objects. The phd format is described in section 10 at this url: http://www.phrap.org/phredphrap/phred.html FEEDBACKMailing ListsUser 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 SupportPlease direct usage questions or support issues to the mailing list: bioperl-l@bioperl.org rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible. Reporting BugsReport 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: https://github.com/bioperl/bioperl-live/issues AUTHOR Chad MatsallaChad Matsalla bioinformatics@dieselwurks.com CONTRIBUTORSJason Stajich, jason@bioperl.org Jean-Marc Frigerio, Frigerio@pierroton.inra.fr APPENDIXThe rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ next_seqTitle : next_seq() Usage : $swq = $stream->next_seq() Function: returns the next phred sequence in the stream Returns : Bio::Seq::Quality object Args : NONE write_headerTitle : write_header() Usage : $seqio->write_header() Function: Write out the header (BEGIN_COMMENTS .. END_COMMENT) part of a phd file Returns : nothing Args : a Bio::Seq::Quality object Notes : These are the comments that reside in the header of a phd file at the present time. If not provided by the Bio::Seq::Quality object, 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 write_seqTitle : write_seq() Usage : $seqio->write_seq($swq); Function: Write out a phd file. Returns : Nothing. Args : a Bio::Seq::Quality object attributeTitle : attribute() Usage : swq->attribute(name[,value]); Function: Get/Set the name attribute. Returns : a string if 1 param, nothing else. Args : a name or a pair name, value chromat_fileTitle : chromat_file Usage : swq->chromat_file([filename]); Function: Get/Set the CHROMAT_FILE attribute. Returns : a string if 1 param, nothing else. Args : none or a filename abi_thumbprintTitle : abi_thumbprint Usage : swq->abi_thumbprint([value]); Function: Get/Set the ABI_THUMBPRINT attribute. Returns : a string if 1 param, nothing else. Args : none or a value phred_versionTitle : phred_version Usage : swq->phred_version([value]); Function: Get/Set the PHRED_VERSION attribute. Returns : a string if 1 param, nothing else. Args : none or a value call_methodTitle : call_method Usage : swq->call_method([value]); Function: Get/Set the CALL_METHOD attribute. Returns : a string if 1 param, nothing else. Args : none or a value quality_levelsTitle : quality_levels Usage : swq->quality_levels([value]); Function: Get/Set the quality_levels attribute. Returns : a string if 1 param, nothing else. Args : none or a value trace_array_min_indexTitle : trace_array_min_index Usage : swq->trace_array_min_index([value]); Function: Get/Set the trace_array_min_index attribute. Returns : a string if 1 param, nothing else. Args : none or a value trace_array_max_indexTitle : trace_array_max_index Usage : swq->trace_array_max_index([value]); Function: Get/Set the trace_array_max_index attribute. Returns : a string if 1 param, nothing else. Args : none or a value chemTitle : chem Usage : swq->chem([value]); Function: Get/Set the chem attribute. Returns : a string if 1 param, nothing else. Args : none or a value dyeTitle : dye Usage : swq->dye([value]); Function: Get/Set the dye attribute. Returns : a string if 1 param, nothing else. Args : none or a value timeTitle : time Usage : swq->time([value]); Function: Get/Set the time attribute. Returns : a string if 1 param, nothing else. Args : none or a value touchTitle : touch Usage : swq->touch(); Function: Set the time attribute to current time. Returns : nothing Args : none
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