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.\"
.IX Title "Bio::Matrix::PSM::IO::masta 3pm"
.TH Bio::Matrix::PSM::IO::masta 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::Matrix::PSM::IO::masta \- motif fasta format parser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
\&\s-1MASTA\s0 is a position frequency matrix format similar to
fasta. It contains one \s-1ID\s0 row just like fasta and then the actual
data, which is tab delimited:
.PP
.Vb 2
\&  0.1   0.62    .017    0.11
\&  0.22  0.13    0.54    0.11
.Ve
.PP
Or A,C,G and T could be horizontally positioned (positioning is
automatically detected).  Please note masta will parse only \s-1DNA\s0 at the
moment.
.PP
It will also convert a set of aligned sequences:
\&\s-1ACATGCAT
ACAGGGAT
ACAGGCAT
ACCGGCAT\s0
.PP
to a \s-1PFM\s0 (SiteMatrix object). When writing if you supply \s-1SEQ\s0 it will
write 10 random instances, which represent correctly the frequency and
can be used as an input for weblogo creation purposes.
.PP
See Bio::Matrix::PSM::IO for detailed documentation on how to use masta parser
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Parser for meme.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Stefan Kirov"
.IX Header "AUTHOR - Stefan Kirov"
Email skirov@utk.edu
.SH "APPENDIX"
.IX Header "APPENDIX"
.SS "new"
.IX Subsection "new"
.Vb 9
\& Title   : new
\& Usage   : my $psmIO =  Bio::Matrix::PSM::IO\->new(\-format=> \*(Aqmasta\*(Aq,
\&                                                 \-file  => $file, 
\&                                                 \-mtype => \*(AqPWM\*(Aq);
\& Function: Associates a file with the appropriate parser
\& Throws  :
\& Example :
\& Args    : hash
\& Returns : "Bio::Matrix::PSM::$format"\->new(@args);
.Ve
.SS "write_psm"
.IX Subsection "write_psm"
.Vb 7
\& 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 :
.Ve
.SS "next_matrix"
.IX Subsection "next_matrix"
.Vb 3
\&  Title   : next_matrix
\&  Usage   : my $matrix = $psmio\->next_matrix;
\&  Function: Alias of next_psm function
.Ve
.SS "next_psm"
.IX Subsection "next_psm"
.Vb 9
\& 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
.Ve