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.\" ========================================================================
.\"
.IX Title "Bio::Tools::Run::MCS 3pm"
.TH Bio::Tools::Run::MCS 3pm "2018-09-14" "perl v5.26.2" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.nh
.SH "NAME"
Bio::Tools::Run::MCS \- Wrapper for MCS
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::Run::MCS;
\&
\&  # Make a MCS factory
\&  $factory = Bio::Tools::Run::MCS\->new();
\&
\&  # Run MCS on an alignment
\&  my @results = $factory\->run($alignfilename);
\&
\&  # or with alignment object
\&  @results = $factory\->run($bio_simplalign);
\&
\&  # look at the results
\&  foreach my $feat (@results) {
\&    my $seq_id = $feat\->seq_id;
\&    my $start = $feat\->start;
\&    my $end = $feat\->end;
\&    my $score = $feat\->score;
\&    my ($pvalue) = $feat\->get_tag_values(\*(Aqpvalue\*(Aq);
\&    my ($kind) = $feat\->get_tag_values(\*(Aqkind\*(Aq); # \*(Aqall\*(Aq, \*(Aqexon\*(Aq or \*(Aqnonexon\*(Aq
\&  }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a wrapper for running the \s-1MCS\s0 (binCons) scripts by Elliott H Margulies.
You can get details here: http://zoo.nhgri.nih.gov/elliott/mcs_doc/. \s-1MCS\s0 is used
for the prediciton of transcription factor binding sites and other regions of
the genome conserved amongst different species.
.PP
Note that this wrapper assumes you already have alignments, so only uses \s-1MCS\s0
for the latter stages (the stages involving align2binomial.pl,
generate_phyloMAX_score.pl and generate_mcs_beta.pl).
.PP
You can try supplying normal \s-1MCS\s0 command-line arguments to \fInew()\fR, eg.
.PP
.Vb 1
\&  $factory\->new(\-percentile => 95)
.Ve
.PP
or calling arg-named methods (excluding the initial
hyphens, eg.
.PP
.Vb 1
\&  $factory\->percentile(95)
\&
\& to set the \-\-percentile arg).
.Ve
.PP
You will need to enable this \s-1MCS\s0 wrapper to find the \s-1MCS\s0 scripts.
This can be done in (at least) three ways:
.PP
.Vb 4
\& 1. Make sure the MCS scripts are in your path.
\& 2. Define an environmental variable MCSDIR which is a 
\&    directory which contains the MCS scripts:
\&    In bash:
\&
\&    export MCSDIR=/home/username/mcs/
\&
\&    In csh/tcsh:
\&
\&    setenv MCSDIR /home/username/mcs
\&
\& 3. Include a definition of an environmental variable MCSDIR in
\&    every script that will use this MCS wrapper module, e.g.:
\&
\&    BEGIN { $ENV{MCSDIR} = \*(Aq/home/username/mcs/\*(Aq }
\&    use Bio::Tools::Run::MCS;
.Ve
.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
the Bioperl mailing list.  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
of the bugs and their resolution. Bug reports can be submitted via
the web:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Sendu Bala"
.IX Header "AUTHOR - Sendu Bala"
Email bix@sendu.me.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns : string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns : string
\& Args    : None
.Ve
.SS "new"
.IX Subsection "new"
.Vb 6
\& Title   : new
\& Usage   : $factory = Bio::Tools::Run::MCS\->new()
\& Function: creates a new MCS factory
\& Returns : Bio::Tools::Run::MCS
\& Args    : Many options understood by MCS can be supplied as key =>
\&           value pairs.
\&
\&           These options can NOT be used with this wrapper:
\&           ucsc gtf neutral\-only fourd\-align align\-only ar
.Ve
.SS "run"
.IX Subsection "run"
.Vb 9
\& Title   : run
\& Usage   : $result = $factory\->run($align_file_or_object, Bio::Location::Atomic,
\&                                   [Bio::SeqFeatureI]);
\& Function: Runs the MCS scripts on an alignment.
\& Returns : list of Bio::SeqFeatureI feature objects (with coordinates corrected
\&           according to the supplied offset, if any)
\& Args    : The first argument represents an alignment, the optional second
\&           argument represents the chromosome, stand and end and the optional
\&           third argument represents annotation of the exons in the alignment.
\&
\&           The alignment can be provided as a multi\-fasta format alignment
\&           filename, or a Bio::Align::AlignI compliant object (eg. a
\&           Bio::SimpleAlign).
\&
\&           The position in the genome can be provided as a Bio::Location::Atomic
\&           with start, end and seq_id set.
\&
\&           The annnotation can be provided as an array of Bio::SeqFeatureI
\&           objects.
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 5
\& Title   : _setparams
\& Usage   : Internal function, not to be called directly
\& Function: Creates a string of params to be used in the command string
\& Returns : string of params
\& Args    : none
.Ve