Bio::EnsEMBL::Analysis::Runnable
RNAFold
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Summary
Bio::EnsEMBL::Analysis::Runnable::RNAfold
Package variables
Privates (from "my" definitions)
$verbose = ""
Included modules
Inherit
Synopsis
my $runnable = Bio::EnsEMBL::Analysis::Runnable::RNAfold->new
(
-analysis => $analysis,
-sequence => $seq,
-structure => $str,
);
$self->runnable($runnable);
Description
Runnble to wrap RNAfold, part of the Vienna RNA package.
Takes a Bio::Seq object and an optional structure string as parameters.
If a structure is provided it uses the structure to constrain the folding
prediction (RNAFold -C).
The resulting structure string is run-length encoded.
Methods
Methods description
Title : RNAfold
Usage : $self->RNAfold($seq,$filename);
Function : Wrapper for RNAfold
Returns : none
Exceptions : Throws if RNAfold fails to run
Args : sequence (Bio::PrimarySeq)
: filename (String) |
Title : encode_str
Usage : my $encoded_str = $runnable->encode_string($string)
Function : Does string length encoding to reduce size of structure string
: splits strings if they are longer then 200 characters so they
: will fit in the transcript attribute table, gives a range value
: at the start of the string indicating the start and stop positions of the
: structure on the transcript
Returns : String
Exceptions : None
Args : String |
Title : encoded_str
Usage : my $str = $runnable->encoded_str
Function : Get/ set for the run-length encoded structure string predicted by RNAfold
Returns : String
Exceptions : None
Args : String |
Title : run
Usage : my $runnable->run;
Function : Run method.
Returns : None
Exceptions : None
Args : None |
Title : parse
Usage : my $structure = $self->parse;
Function : Parses the results of RNAfold
Returns : structure (String)
Exceptions : Throws if results file cannot be opened or closed
Args : None |
Title : score
Usage : my $score = $runnable->score
Function : Get/ set for the score predicted by RNAfold
Returns : String
Exceptions : None
Args : String |
Title : sequence
Usage : my $seq = $runnable->sequence
Function : Get/ set for the sequence object
Returns : Bio::PrimarySeq
Exceptions : Throws if not passed a Bio::PrimarySeq object
Args : BioPrimarySeq |
Title : structure
Usage : my $str = $runnable->structure
Function : Get/ set for the structure string predicted by RNAfold
Returns : String
Exceptions : None
Args : String |
Title : structure_constraint
Usage : my $str = $runnable->structure_constraint
Function : Get/ set for the structure string used by RNAfold to constrain
: the folding prediction
Returns : String
Exceptions : None
Args : String |
Title : write_seq
Usage : my $filename = $self->write_seq($daf);
Function : Writes the dna sequence file
Returns : filename (String)
Exceptions : Throws if it cannot write to the file
Args : Bio::PrimarySeq |
Methods code
sub RNAfold
{ my ($self,$seq,$filename)=@_;
my $command = "RNAfold ";
my $options = "";
if ($self->structure_constraint){
$options = " -C ";
}
my $results_file = $self->create_filename("RNAfold","txt");
$self->files_to_delete($results_file);
$self->files_to_delete("/tmp/".$seq->display_id."_ss.ps");
$self->resultsfile($results_file);
$command .= "$options < $filename 2>&1 > ".$results_file;
print STDERR "Running RNAfold ".$command."\n";
open(my $fh, "$command |") ||
$self->throw("Error opening RNAfold cmd <$command>");
while(<$fh>){
if(/FATAL:(.+)/){
my $match = $1;
$self->throw("miRNA: RNAfold failed to run: $match$@\n");
}
}
close $fh;
return 1;} | sub encode_str
{ my ($self,$string)= @_;
my @codes;
my $start = 1;
my $count=0;
my $code;
my @elements = split //,$string;
my $last_chr = "";
my @array =[];
foreach my $chr (@elements){
$count++;
if ($chr eq $last_chr){
push @array,$chr;
}
else {
if ($code && length($code) > 200 && scalar(@array) == 1){
push @codes,"$start:$count\t$code";
$code = undef;
$start = $count+1;
}
if (scalar(@array) > 1){
$code .= scalar(@array);
@array = [];
}
$code .= "$chr";
$last_chr = $chr;
}
}
if (scalar(@array) > 1){
$code .= scalar(@array);
}
push @codes,"$start:$count\t$code";
return\@ codes;
}
} | sub encoded_str
{ my ($self, $encoded_str) = @_;
if ($encoded_str){
$self->{'_encoded_str'} = $encoded_str;
}
return $self->{'_encoded_str'};} | sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($sequence,$structure) = rearrange(['SEQUENCE','STRUCTURE'], @args);
$self->throw("RNAFold: Cannot work without a sequence object\n") unless $sequence;
$self->sequence($sequence);
$self->structure_constraint($structure) if $structure;
return $self;} | sub parse
{ my ($self)=@_;
my $results = $self->resultsfile;
my $structure;
my $score;
open(RNAFOLD, $results) or $self->throw("FAILED to open ".$results.
" miRNA:parse_results\n$@\n");
LINE: while(<RNAFOLD>){
chomp;
if ($_ =~ /([().]+)\s\(\s*(-*\d+.\d+)\)$/){
$structure = $1;
$score = $2;
}
}
close(RNAFOLD) or $self->throw("FAILED to close ".$results.
" miRNA:parse_results\n$@\n");
$self->score($score);
if ($structure){
return $structure;
} else {
return 0;
}} | sub run
{ my ($self) = @_;
print STDERR "Run analysis\n" if $verbose;
my $filename = $self->write_seq($self->sequence);
$self->RNAfold($self->sequence,$filename);
my $structure = $self->parse;
$self->structure($structure);
$self->encoded_str($self->encode_str($structure));
$self->delete_files; } | sub score
{ my ($self, $score) = @_;
if ($score){
$self->{'_score'} = $score;
}
return $self->{'_score'};
}
1;} | sub sequence
{ my ($self, $sequence) = @_;
if ($sequence){
$self->throw("RNAFold: Sequence needs to be a Bio::PrimarySeq object not a $sequence\n")
unless ($sequence->isa("Bio::PrimarySeq"));
$self->{'_sequence'} = $sequence;
}
return $self->{'_sequence'};} | sub structure
{ my ($self, $structure) = @_;
if ($structure){
$self->{'_structure'} = $structure;
}
return $self->{'_structure'};} | sub structure_constraint
{ my ($self, $structure_constraint) = @_;
if ($structure_constraint){
$self->{'_structure_constraint'} = $structure_constraint;
}
return $self->{'_structure_constraint'};} | sub write_seq
{ my ($self,$seq)=@_;
my $filename = $self->create_filename("miRNA","seq");
$self->files_to_delete("/tmp/$filename");
eval{
open (FILE,">$filename");
print FILE ">".$seq->display_id."\n";
print FILE $seq->seq."\n";
print FILE $self->structure_constraint if ($self->structure_constraint);
close FILE;
};
if ($@){
$self->throw
("RNAFold: Error writing to seq file $@\n");
};
$self->files_to_delete($filename);
return $filename;} | General documentation