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.\" ========================================================================
.\"
.IX Title "Bio::Matrix::PSM::IO::transfac 3pm"
.TH Bio::Matrix::PSM::IO::transfac 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Matrix::PSM::IO::transfac \- PSM transfac parser
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
See Bio::Matrix::PSM::IO for documentation
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
#
.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 8
\& Title   : new
\& Usage   : my $psmIO =  Bio::Matrix::PSM::IO\->new(\-format=>\*(Aqtransfac\*(Aq, 
\&                                                 \-file=>$file);
\& Function: Associates a file with the appropriate parser
\& Throws  :
\& Example :
\& Args    :
\& Returns : "Bio::Matrix::PSM::$format"\->new(@args);
.Ve
.SS "next_psm"
.IX Subsection "next_psm"
.Vb 7
\& Title   : next_psm
\& Usage   : my $psm=$psmIO\->next_psm();
\& Function: Reads the next PSM from the input file, associated with this object
\& Throws  : Upon finding a line, defining the matrix, where one or more positions
\&            are not defined, see _make_matrix
\& Returns : Bio::Matrix::PSM::Psm object
\& Args    : none
.Ve
.SS "_parseMatrix"
.IX Subsection "_parseMatrix"
.Vb 7
\& Title   : _parseMatrix
\& Usage   :
\& Function: Parses a line
\& Throws  :
\& Example :  Internal stuff
\& Returns :  array (frequencies for A,C,G,T in this order).
\& Args    :  string
.Ve
.SS "_make_matrix"
.IX Subsection "_make_matrix"
.Vb 8
\& Title   : _make_matrix
\& Usage   :
\& Function:
\& Throws  :  If a position is undefined, for example if you have line like this
\&            in the file you are parsing: 08  4,7,,9
\& Example :  Internal stuff
\& Returns :
\& Args    :
.Ve