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.\" ========================================================================
.\"
.IX Title "RG::Reprof 3pm"
.TH RG::Reprof 3pm "2012-01-13" "perl v5.14.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
RG::Reprof::Reprof \- protein secondary structure and accessibility predictor
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use RG::Reprof::Reprof;
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
See module commented source for further details.
.SS "Methods"
.IX Subsection "Methods"
.IP "\fI\s-1OBJ\s0\fR RG::Reprof::Reprof\->new( model_dir => \fI\s-1PATH\s0\fR )" 4
.IX Item "OBJ RG::Reprof::Reprof->new( model_dir => PATH )"
Default model_dir: \fI/tmp/lkajan/root/share/reprof\fR.
.Sp
Returns new instance of RG::Reprof::Reprof.
.ie n .IP "\fIint\fR $OBJ\->run( \fBinput_file\fR => \fI\s-1PATH\s0\fR, \fBout_file\fR => \fI\s-1PATH\s0\fR, \fBmutation_file\fR => \fI\s-1PATH\s0\fR, \fBspecific_models\fR => \fIhashref\fR, \fBoutput_func\fR => \fIcoderef\fR )" 4
.el .IP "\fIint\fR \f(CW$OBJ\fR\->run( \fBinput_file\fR => \fI\s-1PATH\s0\fR, \fBout_file\fR => \fI\s-1PATH\s0\fR, \fBmutation_file\fR => \fI\s-1PATH\s0\fR, \fBspecific_models\fR => \fIhashref\fR, \fBoutput_func\fR => \fIcoderef\fR )" 4
.IX Item "int $OBJ->run( input_file => PATH, out_file => PATH, mutation_file => PATH, specific_models => hashref, output_func => coderef )"
.RS 4
.PD 0
.IP "\fBout_file\fR may be a directory." 4
.IX Item "out_file may be a directory."
.IP "\fBmutation_file\fR may be undefined." 4
.IX Item "mutation_file may be undefined."
.IP "\fBspecific_models\fR may be undefined." 4
.IX Item "specific_models may be undefined."
.PD
This is a hash of model and feature files with 'model_name' keys like:
.Sp
.Vb 4
\& {
\&   \*(Aqfub_model\*(Aq => \*(Aq/path/to/model_file\*(Aq,
\&   \*(Aqfub_features\*(Aq => \*(Aq/path/to/features_file\*(Aq
\& }
.Ve
.Sp
Check the module source for the list for model names.
.IP "\fIvoid\fR \fBoutput_func\fR( out_file, sec_pred, acc_pred, sequence ) \- function to call when output is ready." 4
.IX Item "void output_func( out_file, sec_pred, acc_pred, sequence ) - function to call when output is ready."
If undefined, the built-in \fIwrite_output()\fR function is called that prints results to one or more files.  The following positional parameters are passed to this function:
.RS 4
.IP "out_file" 4
.IX Item "out_file"
Output file name.
.IP "sec_pred" 4
.IX Item "sec_pred"
Secondary structure prediction, see source for details.
.IP "acc_pred" 4
.IX Item "acc_pred"
Accessibility prediction, see source for details.
.IP "sequence" 4
.IX Item "sequence"
Reference to array of residues of input sequence (e.g. [ 'M', 'A', 'G', ... ] ).
.RE
.RS 4
.RE
.RE
.RS 4
.RE
.SH "AUTHOR"
.IX Header "AUTHOR"
Original version by Peter Hoenigschmid <hoenigschmid@rostlab.org> and Burkhard Rost.
.PP
Some perl module work and documentation by Laszlo Kajan <lkajan@rostlab.org>.
.SH "SEE ALSO"
.IX Header "SEE ALSO"
<http://rostlab.org/>