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Man Pages


Manual Reference Pages  -  BIO::SEQIO::PHD (3)

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NAME

Bio::SeqIO::phd - phd file input/output stream

CONTENTS

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



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perl v5.20.3 BIO::SEQIO::PHD (3) 2016-04-05

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