/usr/share/perl5/Bio/Tools/Run/FootPrinter.pm is in libbio-perl-run-perl 1.7.1-3.
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#
# Copyright Shawn Hoon
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::FootPrinter - wrapper for the FootPrinter program
=head1 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";
}
}
=head1 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
=head2 About Footprinter
Written by Mathieu Blanchette and Martin Tompa. Available here:
http://www.mcb.mcgill.ca/~blanchem/FootPrinter2.1.tar.gz
=head2 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/
=head2 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)
=head1 FEEDBACK
=head2 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.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
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.
=head2 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/
=head1 AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a "_".
=cut
package Bio::Tools::Run::FootPrinter;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
@FP_SWITCHES @FP_PARAMS @OTHER_SWITCHES %OK_FIELD);
use strict;
use Cwd;
use Bio::Root::Root;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::FootPrinter;
use Bio::SeqIO;
# Let the code begin...
@ISA = qw(Bio::Tools::Run::WrapperBase);
BEGIN {
@FP_PARAMS = qw(SEQUENCE_TYPE SIZE MAX_MUTATIONS MAX_MUTATIONS_PER_BRANCH
LOSSES LOSS_COST TREE PROGRAM SUBREGION_SIZE POSITION_CHANGE_COST
INDEL_COST INVERSION_COST );
@FP_SWITCHES = qw(TRIPLET_FILTERING PAIR_FILTERING POST_FILTERING DETAILS);
@OTHER_SWITCHES = qw(QUIET HTML PS);
# Authorize attribute fields
foreach my $attr ( @FP_PARAMS, @FP_SWITCHES,
@OTHER_SWITCHES) { $OK_FIELD{$attr}++; }
}
=head2 program_name
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
=cut
sub program_name {
return 'FootPrinter';
}
=head2 program_dir
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
=cut
sub program_dir {
return Bio::Root::IO->catfile($ENV{FOOTPRINTER_DIR}) if $ENV{FOOTPRINTER_DIR};
}
=head2 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
=cut
sub executable {
my $self = shift;
my $exe = $self->SUPER::executable(@_) || return;
# even if its executable, we still need the environment variable to have
# been set
if (! $ENV{FOOTPRINTER_DIR}) {
$self->warn("Environment variable FOOTPRINTER_DIR must be set, even if the FootPrinter executable is in your path");
return;
}
return $exe;
}
sub AUTOLOAD {
my $self = shift;
my $attr = $AUTOLOAD;
$attr =~ s/.*:://;
$attr = uc $attr;
$self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
$self->{$attr} = shift if @_;
return $self->{$attr};
}
=head2 new
Title : new
Usage : $rm->new($seq)
Function: creates a new wrapper
Returns: Bio::Tools::Run::FootPrinter
Args : self
=cut
sub new {
my ($class, @args) = @_;
my $self = $class->SUPER::new(@args);
my ($attr, $value);
while (@args) {
$attr = shift @args;
$value = shift @args;
next if( $attr =~ /^-/ ); # don't want named parameters
$self->$attr($value);
}
if(!$self->tree && -e $ENV{FOOTPRINTER_DIR}."/tree_of_life"){
$self->tree($ENV{FOOTPRINTER_DIR}."/tree_of_life");
}
unless($self->tree){
$self->debug("Phylogenetic tree not provided. FootPrinter won't be able to run without it. use \$fp->tree to set the tree file");
}
return $self;
}
=head2 run
Title : run
Usage : $fp->run(@seq)
Function: carry out FootPrinter
Example :
Returns : An array of SeqFeatures
Args : An array of Bio::PrimarySeqI compliant object
At least 2 are needed.
=cut
sub run {
my ($self,@seq) = @_;
#need at least 2 for comparative genomics duh.
$#seq > 0 || $self->throw("Need at least two sequences");
$self->tree || $self->throw("Need to specify a phylogenetic tree using -tree option");
my $infile = $self->_setinput(@seq);
my $param_string = $self->_setparams();
my @footprint_feats = $self->_run($infile,$self->tree,$param_string);
return @footprint_feats;
}
=head2 _run
Title : _run
Usage : $fp->_run ($filename,$param_string)
Function: internal function that runs FootPrinter
Example :
Returns : an array of features
Args : the filename to the input sequence, filename to phylo tree
and the parameter string
=cut
sub _run {
my ($self,$infile,$tree,$param_string) = @_;
my $instring;
my $exe = $self->executable || return;
$self->debug( "Program ".$self->executable."\n");
my $outfile = $infile.".seq.txt";
my $cmd_str = $self->executable. " $infile $tree $param_string";
$self->debug("FootPrinter command = $cmd_str");
if ($self->verbose <=0){
my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';
$cmd_str.= " >&$null > $null";
}
# will do brute-force clean up of junk files generated by FootPrinter
my $cwd = cwd();
opendir(my $cwd_dir, $cwd) || $self->throw("Could not open the current directory '$cwd'!");
my %ok_files;
foreach my $thing (readdir($cwd_dir)) {
if ($thing =~ /^mlc\./) {
$ok_files{$thing} = 1;
}
}
closedir($cwd_dir);
my $status = system($cmd_str);
$self->throw("FootPrinter Call($cmd_str) crashed: $?\n")
unless $status == 0 || $status==256;
unless (open (FP, $outfile)) {
$self->throw("Cannot open FootPrinter outfile for parsing");
}
my $fp_parser = Bio::Tools::FootPrinter->new(-fh=>\*FP);
my @fp_feat;
while(my $fp_feat = $fp_parser->next_feature){
push @fp_feat, $fp_feat;
}
unless( $self->save_tempfiles ) {
unlink $outfile;
unlink $infile; # is this dangerous??
unlink "$infile.order.txt"; # is this dangerous??
opendir($cwd_dir, $cwd) || $self->throw("Could not open the current directory '$cwd'!");
foreach my $thing (readdir($cwd_dir)) {
if ($thing =~ /^mlc\./) {
unlink($thing) unless $ok_files{$thing};
}
}
closedir($cwd_dir);
$self->cleanup();
}
return @fp_feat;
}
=head2 _setparams()
Title : _setparams
Usage : Internal function, not to be called directly
Function: Create parameter inputs for FootPrinter program
Example :
Returns : parameter string to be passed to FootPrinter
Args : name of calling object
=cut
sub _setparams {
my ($attr, $value, $self);
$self = shift;
my $param_string = "";
for $attr ( @FP_PARAMS ) {
$value = $self->$attr();
next if $attr=~/TREE/i;
next unless (defined $value);
my $attr_key = lc $attr; #put params in format expected by dba
if ($attr_key eq 'losses' && $value =~ /^\s*(somewhat|very)?\s*significant\s*$/) {
$value = "$ENV{FOOTPRINTER_DIR}/universal".$self->size();
if (defined $1) {
if ($1 eq 'somewhat') {
$value .= 'loose';
} else { # $1 eq 'very'
$value .= 'tight';
}
}
$value .= '.config';
-f $value or $self->throw("universal losses file $value does not exist");
}
$attr_key = ' -'.$attr_key;
$param_string .= $attr_key.' '.$value;
}
for $attr ( @FP_SWITCHES) {
$value = $self->$attr();
next unless ($value);
my $attr_key = lc $attr; #put switches in format expected by dba
$attr_key = ' -'.$attr_key;
$param_string .= $attr_key ;
}
$self->html() or $param_string .= " -no_html";
$self->ps() or $param_string .= " -no_ps";
return $param_string;
}
=head2 _setinput()
Title : _setinput
Usage : Internal function, not to be called directly
Function: writes input sequence to file and return the file name
Example :
Returns : string
Args : a Bio::PrimarySeqI compliant object
=cut
sub _setinput {
my ($self,@seq) = @_;
my ($tfh1,$outfile1);
$outfile1 = $self->outfile_name();
if (defined $outfile1) {
open($tfh1,">$outfile1");
} else {
($tfh1,$outfile1) = $self->io->tempfile(-dir=>$self->tempdir);
}
my $out1 = Bio::SeqIO->new('-fh' => $tfh1,
'-format' => 'Fasta');
foreach my $seq(@seq){
$seq->isa("Bio::PrimarySeqI") || $self->throw("Need a Bio::PrimarySeq compliant object for FootPrinter");
$out1->write_seq($seq);
}
$out1->close(); # close the SeqIO object
close($tfh1); # close the fh explicitly (just in case)
undef($tfh1); # really get rid of it (just in case)
return ($outfile1);
}
=head1 Bio::Tools::Run::Wrapper methods
=cut
=head2 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)
=cut
=head2 save_tempfiles
Title : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
=cut
=head2 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
=cut
=head2 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
=cut
=head2 cleanup
Title : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory
Returns : none
Args : none
=cut
=head2 io
Title : io
Usage : $obj->io($newval)
Function: Gets a L<Bio::Root::IO> object
Returns : L<Bio::Root::IO>
Args : none
=cut
1;
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