Bio::AlignIO::meme(3pm) User Contributed Perl Documentation Bio::AlignIO::meme(3pm)NAME
Bio::AlignIO::meme - meme sequence input/output stream
SYNOPSIS
Do not use this module directly. Use it via the Bio::AlignIO class.
use Bio::AlignIO;
# read in an alignment from meme
my $in = Bio::AlignIO->new(-format => 'meme',
-file => 'meme.out');
while( my $aln = $in->next_aln ) {
# do something with the alignment
}
DESCRIPTION
This object transforms the "sites sorted by position p-value" sections of a meme (text) output file into a series of Bio::SimpleAlign
objects. Each SimpleAlign object contains Bio::LocatableSeq objects which represent the individual aligned sites as defined by the central
portion of the "site" field in the meme file. The start and end coordinates are derived from the "Start" field. See Bio::SimpleAlign and
Bio::LocatableSeq for more information.
This module can only parse MEME version 3.0 and greater. Previous versions have output formats that are more difficult to parse correctly.
If the meme output file is not version 3.0 or greater, we signal an error.
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://redmine.open-bio.org/projects/bioperl/
AUTHORS - Benjamin Berman
Bbased on the Bio::SeqIO modules by Ewan Birney and others
Email: benb@fruitfly.berkeley.edu
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with an underscore.
next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : Bio::SimpleAlign object with the score() set to the evalue of the
motif.
Args : NONE
write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: Not implemented
Returns : 1 for success and 0 for error
Args : Bio::SimpleAlign object
perl v5.14.2 2012-03-02 Bio::AlignIO::meme(3pm)
Check Out this Related Man Page
Bio::AlignIO::maf(3pm) User Contributed Perl Documentation Bio::AlignIO::maf(3pm)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, "
";
print $aln->length, "
";
print $aln->num_residues, "
";
print $aln->is_flush, "
";
print $aln->num_sequences, "
";
$aln->splice_by_seq_pos(1);
print $aln->consensus_string(60), "
";
print $aln->get_seq_by_pos(1)->seq, "
";
print $aln->match_line(), "
";
print "
";
}
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://redmine.open-bio.org/projects/bioperl/
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 v5.14.2 2012-03-02 Bio::AlignIO::maf(3pm)