Christopher Fields > BioPerl > Bio::AlignIO::pfam

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Module Version: 1.006924   Source  

NAME ^

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

SYNOPSIS ^

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

DESCRIPTION ^

This object can transform Bio::SimpleAlign objects to and from pfam flat file databases.

FEEDBACK ^

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

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 _

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 $aln object into the stream
 Returns : 1 for success and 0 for error
 Args    : L<Bio::Align::AlignI> object
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