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Bio::SeqIO::phd(3)    User Contributed Perl Documentation   Bio::SeqIO::phd(3)

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://github.com/bioperl/bioperl-live/issues

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 v5.32.1			  2019-12-07		    Bio::SeqIO::phd(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR Chad Matsalla | CONTRIBUTORS | APPENDIX

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