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Bio::SeqIO::phd.3pm
Langue: en
Version: 2010-05-19 (ubuntu - 24/10/10)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::SeqIO::phd - .phd file input/output streamSYNOPSIS
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 objectsFEEDBACK
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Support
Please 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 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.comCONTRIBUTORS
Jason Stajich, jason@bioperl.org Jean-Marc Frigerio, Frigerio@pierroton.inra.frAPPENDIX
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_header
Title : 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_seq
Title : write_seq() Usage : $seqio->write_seq($swq); Function: Write out a phd file. Returns : Nothing. Args : a Bio::Seq::Quality object
attribute
Title : 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_file
Title : 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_thumbprint
Title : 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_version
Title : 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_method
Title : 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_levels
Title : 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_index
Title : 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_index
Title : 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
chem
Title : chem Usage : swq->chem([value]); Function: Get/Set the chem attribute. Returns : a string if 1 param, nothing else. Args : none or a value
dye
Title : dye Usage : swq->dye([value]); Function: Get/Set the dye attribute. Returns : a string if 1 param, nothing else. Args : none or a value
time
Title : time Usage : swq->time([value]); Function: Get/Set the time attribute. Returns : a string if 1 param, nothing else. Args : none or a value
touch
Title : touch Usage : swq->touch(); Function: Set the time attribute to current time. Returns : nothing Args : none
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