Bio::Matrix::PSM::IO::UseraContributed Perl DocuBio::Matrix::PSM::IO::masta(3)NAMEBio::Matrix::PSM::IO::masta - motif fasta format parser
SYNOPSIS
MASTA is a position frequency matrix format similar to fasta. It
contains one ID row just like fasta and then the actual data, which is
tab delimited:
0.1 0.62 .017 0.11
0.22 0.13 0.54 0.11
Or A,C,G and T could be horizontally positioned (positioning is
automatically detected). Please note masta will parse only DNA at the
moment.
It will also convert a set of aligned sequences: ACATGCAT ACAGGGAT
ACAGGCAT ACCGGCAT
to a PFM (SiteMatrix object). When writing if you supply SEQ it will
write 10 random instances, which represent correctly the frequency and
can be used as an input for weblogo creation purposes.
See Bio::Matrix::PSM::IO for detailed documentation on how to use masta
parser
DESCRIPTION
Parser for meme.
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 one of the Bioperl mailing lists. Your participation is much
appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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/
AUTHOR - Stefan Kirov
Email skirov@utk.edu
APPENDIX
new
Title : new
Usage : my $psmIO = Bio::Matrix::PSM::IO->new(-format=> 'masta',
-file => $file,
-mtype => 'PWM');
Function: Associates a file with the appropriate parser
Throws :
Example :
Args : hash
Returns : "Bio::Matrix::PSM::$format"->new(@args);
write_psm
Title : write_psm
Usage :
Function: writes a pfm/pwm/raw sequence in a simple masta format
Throws :
Example :
Args : SiteMatrix object, type (optional string: PWM, SEQ or PFM)
Returns :
next_matrix
Title : next_matrix
Usage : my $matrix = $psmio->next_matrix;
Function: Alias of next_psm function
next_psm
Title : next_psm
Usage : my $matrix=$psmio->next_psm;
Function: returns the next matrix in the stream
Throws : If there is you mix different types, for example weights and
frequencies occur in the same entry You can mix weights, but these
should be designated by different ID lines
Example :
Args :
Returns : Bio::Matrix::PSM::SiteMatrix
perl v5.14.1 2011-07-22 Bio::Matrix::PSM::IO::masta(3)