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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

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:

   http://bugzilla.open-bio.org/
 
 

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
  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