Bio::Tools::Run::FootPrinter - Wrapper for FootPrinter Program 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, 'program'=>"/usr/users/shawnh/software/FootPrinter2.0/FootPrinter", 'tree' =>"/usr/users/shawnh/software/FootPrinter2.0/tree_of_life", 'verbose'=>1); my $fp = Bio::Tools::Run::FootPrinter->new(@params); my $sio = Bio::SeqIO->new(-file=>"/usr/users/shawnh/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"; } } Taken from 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 Copyright (c) 1999-2002, by Mathieu Blanchette and Martin Tompa. http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput.pl **NOTE** To run FootPrinter, you will need to set the enviroment variable FOOTPRINTER_DIR to where the binary is located. 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 doesn't 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)

Mailing Lists
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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://bugzilla.bioperl.org/ Email shawnh@fugu-sg.org 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, obtiained from ENV variable. Returns: string Args :

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

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