Bio::AlignIO::maf(3) User Contributed Perl Documentation Bio::AlignIO::maf(3)NAMEBio::AlignIO::maf - Multiple Alignment Format sequence input stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
use Bio::AlignIO;
my $alignio = Bio::AlignIO->new(-fh => \*STDIN, -format => 'maf');
while(my $aln = $alignio->next_aln()){
my $match_line = $aln->match_line;
print $aln, "\n";
print $aln->length, "\n";
print $aln->num_residues, "\n";
print $aln->is_flush, "\n";
print $aln->num_sequences, "\n";
$aln->splice_by_seq_pos(1);
print $aln->consensus_string(60), "\n";
print $aln->get_seq_by_pos(1)->seq, "\n";
print $aln->match_line(), "\n";
print "\n";
}
DESCRIPTION
This class constructs Bio::SimpleAlign objects from an MAF-format
multiple alignment file.
Writing in MAF format is currently unimplemented.
Spec of MAF format is here:
http://genome.ucsc.edu/FAQ/FAQformat
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:
http://bugzilla.open-bio.org/
AUTHORS - Allen Day
Email: allenday@ucla.edu
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $alignio = Bio::AlignIO->new(-format => 'maf'
-file => '>file',
-idlength => 10,
-idlinebreak => 1);
Function: Initialize a new L<Bio::AlignIO::maf> reader
Returns : L<Bio::AlignIO> object
Args :
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream.
Throws an exception if trying to read in PHYLIP
sequential format.
Returns : L<Bio::SimpleAlign> object
Args :
perl v5.14.1 2011-07-22 Bio::AlignIO::maf(3)
