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Bio::AlignIO::emboss.3pm

NAME

Bio::AlignIO::emboss - Parse EMBOSS alignment output (from applications water and needle)

SYNOPSIS

     # do not use the object directly
     use Bio::AlignIO;
     # read in an alignment from the EMBOSS program water
     my $in = Bio::AlignIO->new(-format => 'emboss',
                               -file   => 'seq.water');
     while( my $aln = $in->next_aln ) {
     # do something with the alignment
     }
 
 

DESCRIPTION

This object handles parsing and writing pairwise sequence alignments from the EMBOSS suite.

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 the Bioperl mailing list. 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 of the bugs and their resolution. Bug reports can be submitted via the web:

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

AUTHOR - Jason Stajich

Email jason@bioperl.org

APPENDIX

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

next_aln

  Title   : next_aln
  Usage   : $aln = $stream->next_aln()
  Function: returns the next alignment in the stream.
  Returns : L<Bio::Align::AlignI> object - returns 0 on end of file
             or on error
  Args    : NONE
 
 

write_aln

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