Bio::SeqIO::abi.3pm

Langue: en

Version: 2009-02-27 (fedora - 05/07/09)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::SeqIO::abi - abi trace sequence input/output stream

SYNOPSIS

Do not use this module directly. Use it via the Bio::SeqIO class.

DESCRIPTION

This object can transform Bio::Seq objects to and from abi trace files. To optionally read the trace graph data (which can be used to draw chromatographs, for instance), set the optional '-read_graph_data' flag or the read_graph_data method to a value evaluating to TRUE.

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
 
 

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/
 
 

AUTHORS - Aaron Mackey

Email: amackey@virginia.edu

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   : $seq = $stream->next_seq()
  Function: returns the next sequence in the stream
  Returns : Bio::Seq::Quality object
  Args    : NONE
 
 

write_seq

  Title   : write_seq
  Usage   : $stream->write_seq(@seq)
  Function: writes the $seq object into the stream
  Returns : 1 for success and 0 for error
  Args    : Bio::Seq object
 
 

get_trace_data

  Title   : get_trace_data
  Usage   : $stream->get_trace_data(1)
  Function: set boolean flag to retrieve the trace data (possibly for
            output)
  Returns : bool value, TRUE = retrieve trace data (default FALSE)
  Args    : bool value