NAME¶
Bio::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:
https://github.com/bioperl/bioperl-live/issues
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 :