Bio::SeqIO::phd(3pm) User Contributed Perl Documentation Bio::SeqIO::phd(3pm)
NAME
Bio::SeqIO::phd - phd file input/output stream
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.html
FEEDBACK
Mailing Lists
User 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
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:
https://redmine.open-bio.org/projects/bioperl/
AUTHOR Chad Matsalla
Chad Matsalla bioinformatics@dieselwurks.com
CONTRIBUTORS
Jason Stajich, jason@bioperl.org Jean-Marc Frigerio, Frigerio@pierroton.inra.fr
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
perl v5.14.2 2012-03-02 Bio::SeqIO::phd(3pm)