Ewan Birney

NAME

Bio::AlignIO::clustalw - clustalw sequence input/output stream

SYNOPSIS

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

DESCRIPTION

This object can transform Bio::Align::AlignI objects to and from clustalw flat file databases.

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://bio.perl.org/MailList.html   - 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 email or the web:

  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/

AUTHORS - Peter Schattner

Email: schattner@alum.mit.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : $alignio = new Bio::AlignIO(-format => 'clustalw', 
                                       -file => 'filename');
 Function: returns a new Bio::AlignIO object to handle clustalw files
 Returns : Bio::AlignIO::clustalw object
 Args    : -verbose => verbosity setting (-1,0,1,2)
           -file    => name of file to read in or with ">" - writeout
           -fh      => alternative to -file param - provide a filehandle 
                       to read from/write to 
           -format  => type of Alignment Format to process
           -percentages => (clustalw only) display a percentage of identity
                           in each line of the alignment.

next_aln

 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream
 Returns : L<Bio::Align::AlignI> object
 Args    : NONE

write_aln

 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the clustalw-format object (.aln) into the stream
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object

percentages

 Title   : percentages
 Usage   : $obj->percentages($newval)
 Function: Set the percentages flag - whether or not to show percentages in 
           each output line
 Returns : value of percentages
 Args    : newvalue (optional)