SYNOPSIS
use Bio::Tools::Run::FootPrinter;
my @params = (size => 10,
max_mutations_per_branch => 4,
sequence_type => 'upstream',
subregion_size => 30,
position_change_cost => 5,
triplet_filtering => 1,
pair_filtering => 1,
post_filtering => 1,
inversion_cost => 1,
max_mutations => 4,
tree => "~/software/FootPrinter2.0/tree_of_life" );
my $fp = Bio::Tools::Run::FootPrinter->new(@params, -verbose => 1);
my $sio = Bio::SeqIO->new(-file => "seq.fa", -format => "fasta");
while (my $seq = $sio->next_seq){
push @seq, $seq;
}
my @fp = $fp->run(@seq);
foreach my $result(@fp){
print "***************\n".$result->seq_id."\n";
foreach my $feat($result->sub_SeqFeature){
print $feat->start."\t".$feat->end."\t".$feat->seq->seq."\n";
}
}
DESCRIPTION
From the FootPrinter manual:FootPrinter is a program that performs phylogenetic footprinting. It takes as input a set of unaligned orthologous sequences from various species, together with a phylogenetic tree relating these species. It then searches for short regions of the sequences that are highly conserved, according to a parsimony criterion.
The regions identified are good candidates for regulatory elements. By default, the program searches for regions that are well conserved across all of the input sequences, but this can be relaxed to find regions conserved in only a subset of the species
About Footprinter
Written by Mathieu Blanchette and Martin Tompa. Available here:
http://www.mcb.mcgill.ca/~blanchem/FootPrinter2.1.tar.gz
Running Footprinter
To run FootPrinter, you will need to set the environment variable FOOTPRINTER_DIR to where the binary is located (even if the executable is in your path). For example:
setenv FOOTPRINTER_DIR /usr/local/bin/FootPrinter2.0/
Available Parameters
PARAM VALUES DESCRIPTION
------------------------------------------------------------------------
tree <file> REQUIRED, Tree in Newick Format
to evaluate parsimony score
REQUIRED unless tree_of_life
exists in FOOTPRINTER_DIR
sequence_type upstream Default upstream
downstream
other
size 4-16 Specifies the size of the motifs sought
max_mutations 0-20 maximum parsimony score allowed for the motifs
max_mutations_per_branch 0-20 Allows at most a fixed number of mutations per
branch of the tree
losses <file> files give span constraints so that the motifs
reported are statistically significant
Example files
universal([6-9]|1[0-2])(loose|tight)?.config
come with FootPrinter2.0.
Install these in FOOTPRINTER_DIR and use by
setting "losses" to "somewhat significant",
"significant", or "very significant". Do not
set loss_cost.
loss_cost 0-20 a cost associated with losing a motif along some
branch of the tre
subregion_size 1-infinity penalize motifs whose position in the sequences
varies too much
position_change_cost 0-20 Cost for changing subregion
triplet_filtering 1/0 pre-filtering step that removes from consideration
any substring that does not have a sufficiently good
pair of matching substrings in some pair of the other
input sequences
pair_filtering 1/0 Same as triplet filtering, but looks only for one match
per other sequence
post_filtering 1/0 when used in conjunction with the triplet filtering
option, this often significantly speeds up the program,
while still garanteeing optimal results
indel_cost 1-5 insertions and deletions will be allowed in the motifs
sought, at the given cost
inversion_cost 1-5 This option allows for motifs to undergo inversions,
at the given cost. An inversion reverse-complements
the motif.
details 1/0 Shows some of the details about the progress of the
computation
html 1/0 produce html output (never deleted)
ps 1/0 produce postscript output (never deleted)
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.
[email protected] - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list: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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Shawn Hoon
Email [email protected]APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a ``_''.program_name
Title : program_name Usage : $factory>program_name() Function: holds the program name Returns: string Args : None
program_dir
Title : program_dir Usage : $factory->program_dir(@params) Function: returns the program directory, obtained from ENV variable. Returns: string Args :
executable
Title : executable
Usage : my $exe = $footprinter->executable('FootPrinter');
Function: Finds the full path to the 'FootPrinter' executable
Returns : string representing the full path to the exe
Args : [optional] name of executable to set path to
[optional] boolean flag whether or not warn when exe is not found
new
Title : new Usage : $rm->new($seq) Function: creates a new wrapper Returns: Bio::Tools::Run::FootPrinter Args : self
run
Title : run
Usage : $fp->run(@seq)
Function: carry out FootPrinter
Example :
Returns : An array of SeqFeatures
Args : An array of Bio::PrimarySeqI compliant object
At least 2 are needed.
_run
Title : _run
Usage : $fp->_run ($filename,$param_string)
Function: internal function that runs FootPrinter
Example :
Returns : an array of features
Args : the filename to the input sequence, filename to phylo tree
and the parameter string
_setparams()
Title : _setparams Usage : Internal function, not to be called directly Function: Create parameter inputs for FootPrinter program Example : Returns : parameter string to be passed to FootPrinter Args : name of calling object
_setinput()
Title : _setinput Usage : Internal function, not to be called directly Function: writes input sequence to file and return the file name Example : Returns : string Args : a Bio::PrimarySeqI compliant object
Bio::Tools::Run::Wrapper methods
no_param_checks
Title : no_param_checks
Usage : $obj->no_param_checks($newval)
Function: Boolean flag as to whether or not we should
trust the sanity checks for parameter values
Returns : value of no_param_checks
Args : newvalue (optional)
save_tempfiles
Title : save_tempfiles Usage : $obj->save_tempfiles($newval) Function: Returns : value of save_tempfiles Args : newvalue (optional)
outfile_name
Title : outfile_name
Usage : my $outfile = $codeml->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
tempdir
Title : tempdir Usage : my $tmpdir = $self->tempdir(); Function: Retrieve a temporary directory name (which is created) Returns : string which is the name of the temporary directory Args : none
cleanup
Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory Returns : none Args : none
io
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none