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. The phd format is described in section 10 at this url: http://www.phrap.org/phredphrap/phred.htmlFEEDBACK
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AUTHOR Chad Matsalla
Chad Matsalla [email protected]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
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