Bio::EnsEMBL::Analysis::Runnable::Finished
GenewiseHmm
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Summary
Bio::EnsEMBL::Analysis::Runnable::Finished::GenewiseHmm
- Hmms to genomic sequence
Package variables
Privates (from "my" definitions)
$options = { 'Algorithm type: ' => undef, 'Search algorithm used: ' => undef, 'Implementation: ' => undef, 'Search mode: ' => undef, 'Protein info from: ' => undef, 'Dna info from: ' => undef, 'Start/End (protein) ' => undef, 'Gene Paras: ' => undef, 'Codon Table: ' => undef, 'Subs error: ' => undef, 'Indel error: ' => undef, 'Model splice? ' => undef, 'Model codon bias? ' => undef, 'Model intron bias? ' => undef, 'Null model ' => undef, 'Alignment Alg ' => undef }
Included modules
Inherit
Synopsis
# Initialise the GenewiseHmm module
my $genewise = new Bio::EnsEMBL::Analysis::Runnable::Finished::GenewiseHmm ('query' => $genomic,
'hmmfile' => $hmmfile,
'memory' => $memory);
$genewise->run;
my @genes = $blastwise->output
Description
This module is created and run by halfwisehmm.pm, it takes a pfam hmm and some genomic sequence and runs genewise using these then parses the output to produce
feature pairs representing the genes with exons as subseq features and supporting evidence as subseqfeatures of the exons
Methods
Methods description
Arg [1] : path to directory output files are to be written too
Function : runs genewise and parse output producing arrays of genes, exons and supporting features
Returntype: none
Exceptions: throws if problems opening or closing pipe to genewise
Caller :
Example : |
Arg [1] : Bio:EnsEMBL::SeqFeature
Function : adds the seqfeature to the output array
Returntype: none
Exceptions: throws if not passed a seqfeature
Caller :
Example : |
Arg [1] : array ref of Bio:EnsEMBL::SeqFeature
Function : adds the seqfeatures to the output array like addGene does for singles
Returntype: none
Exceptions: throws if not passed a seqfeature
Caller :
Example : |
Title : hmmfile
Usage : $obj->hmmfile($newval)
Function:
Returns : value of hmmfile
Args : newvalue (optional) |
Args : Bio::Seq, int, boolean, boolean, path, filename
Function : create a Finished_GenewiseHmm object
Returntype: object created
Exceptions: throws if give no query sequence or no hmmfile
Caller :
Example : |
Arg [1] : none
Function : returns the output array
Returntype:
Exceptions: none
Caller :
Example : |
Arg [1] : path to directory outputfiles are to be written too
Function : calls methods which run genewise
Returntype: none
Exceptions: none
Caller :
Example : |
Arg [1] : none
Function : check that the WISECONFIGDIR is set
Returntype: none
Exceptions: thows if variable isn't a directory'
Caller :
Example : |
Methods code
sub _align_protein
{ my ( $self, $dir ) = @_;
my $memory = $self->memory;
$self->workdir('/tmp') unless ( $self->workdir($dir) );
$self->checkdir();
my $genfile = "gw." . $$ . ".gen.fa";
$self->write_fasta($genfile);
my $hmm = $self->hmmfile;
my $genewise = $self->genewise;
$self->files_to_delete($genfile);
$self->files_to_delete($hmm);
my $command =
"$genewise $hmm $genfile " . $self->options() . $self->memory();
$command .= " -init endbias -splice flat "
if ( $self->endbias && $self->endbias == 1 );
$command .= " -trev " if ( $self->is_reverse && $self->is_reverse == 1 );
print STDERR "Command is $command\n";
local $/ = "//\n";
open( my $fh, "$command 2>&1 |" )
or throw("error piping to genewise: $!\n");
while (<$fh>) {
if(/Out of memory/) {
$self->delete_files;
die qq{"OUT_OF_MEMORY"\n};
}
my ( $header, $results ) = split( "\n>", $_ );
$self->parse_headers($header) if $header;
my $genes = $self->parse_alignments($results);
$self->addGenes($genes);
}
close($fh) or throw("Error running genewise:$!\n");
print "there are ",
scalar( $self->output )
. " genes predicted using hmms in file "
. $hmm . "\n";
$self->delete_files;
} | sub addGene
{ my ( $self, $arg ) = @_;
if ( $arg->isa("Bio::EnsEMBL::SeqFeature") ) {
push( @{ $self->{'_output'} }, $arg );
}
else {
throw("this, $arg, should be a seqfeature\n");
}
} | sub addGenes
{ my ( $self, $args ) = @_;
foreach my $arg (@$args) {
if ( $arg->isa("Bio::EnsEMBL::SeqFeature") ) {
push( @{ $self->{'_output'} }, $arg );
}
else {
throw("this, $arg, should be a seqfeature\n");
}
}
}
} | sub endbias
{ my ( $self, $boolean ) = @_;
$self->{'_endbias'} = ( $boolean == 1 ? $boolean : 0 ) if $boolean;
return $self->{'_endbias'};} | sub genewise
{ my ( $self, $arg ) = @_;
$self->{_genewise} = $arg if $arg;
return $self->{_genewise};
}
} | sub get_score
{ my ( $self, $p, $s ) = @_;
return $self->{'_scores'}->{$p}->{$s};
}
1;} | sub gw_options
{ my ( $self, $option_name, $option_value ) = @_;
unless ( $self->{'_gw_options'} ) {
$self->{'_gw_options'} = $self->valid_options;
}
$self->{'_gw_options'}->{$option_name} = $option_value if $option_value;
return $self->{'_gw_options'}->{$option_name};} | sub hmmfile
{ my ( $self, $file ) = @_;
$self->{'hmmfile'} = $file if $file;
return $self->{'hmmfile'};
}
} | sub is_reverse
{ my ( $self, $boolean ) = @_;
$self->{'_reverse'} = ( $boolean == 1 ? $boolean : 0 ) if $boolean;
return $self->{'_reverse'};} | sub memory
{ my ( $self, $arg ) = @_;
$self->{'_memory'} = ' -kbyte ' . $arg if $arg;
return $self->{'_memory'} || ' -kbyte 100000';} | sub new
{ my ( $class, @args ) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_output'} = [];
$self->{'_reverse'} = undef;
my ( $query, $memory, $reverse, $endbias, $genewise, $hmmfile, $options ) =
rearrange( [qw(QUERY MEMORY REVERSE ENDBIAS GENEWISE HMMFILE OPTIONS)],
@args );
$genewise ||= 'genewise';
$options ||= '-ext 2 -genes';
$self->genewise( $self->program($genewise) );
$self->query($query) || throw("No query sequence entered for blastwise");
$self->hmmfile($hmmfile) || throw("No Hmm file entered for Hmmgenewise");
$self->is_reverse($reverse) if ( defined($reverse) );
$self->endbias($endbias) if ( defined($endbias) );
$self->memory($memory) if ( defined($memory) );
$self->options($options);
return $self;
}
} | sub output
{ my ($self) = @_;
return @{ $self->{'_output'} };} | sub parse_alignments
{ my $self = shift;
my @results = split( "\n", +shift );
my $firstline = shift(@results);
pop(@results) if $results[-1] eq '//';
my ( $pdomain, $clone, $strand, $count, $gff_strand );
if ( $firstline =~
m!Results for (.+) vs (.+) \((forward|reverse)\) \[(\d)\]! )
{
$pdomain = $1;
$clone = $2;
$strand = ( $3 eq 'forward' ? 1 : -1 );
$gff_strand = ( $3 eq 'forward' ? '+' : '-' );
$count = $4;
}
else {
warning("couldn't read firstline <$firstline>");
}
my $score = $self->get_score( $pdomain, "[$gff_strand]" );
my @genes;
my $allowed = { 'Gene' => 1, 'Exon' => 1, 'Supporting' => 1 };
foreach (@results) {
my @F = split;
next unless ( defined $F[0] && $allowed->{ $F[0] } );
my $check = 1;
if ( $F[0] eq 'Gene' && $F[1] && $F[2] && !( $F[1] eq 'Paras:' ) ) {
( $F[1], $F[2], $check ) = ( $F[2], $F[1], -1 ) if $F[2] < $F[1];
if ( $check == $strand ) {
my $gene = Bio::EnsEMBL::SeqFeature->new();
$gene->id($clone);
$gene->seqname($pdomain);
push( @genes, $gene );
}
else { warning "strands don't match" }
}
elsif ( $F[0] eq 'Exon' ) {
( $F[1], $F[2], $check ) = ( $F[2], $F[1], -1 ) if $F[2] < $F[1];
if ( $check == $strand ) {
my $exon = Bio::EnsEMBL::SeqFeature->new();
$exon->seqname($clone);
$exon->id($pdomain);
$exon->start( $F[1] );
$exon->end( $F[2] );
$exon->strand($strand);
$genes[-1]->add_sub_SeqFeature( $exon, 'EXPAND' );
}
else { warning "strands don't match" }
}
elsif ( $F[0] eq 'Supporting' ) {
( $F[1], $F[2], $check ) = ( $F[2], $F[1], -1 ) if $F[2] < $F[1];
if ( $check == $strand ) { }
}
else { }
}
return\@ genes; } | sub parse_headers
{ my $self = shift;
my @header = split( "\n", +shift );
local $" = "\n";
my $information = $self->valid_options();
foreach my $line (@header) {
if ( $line =~ m!([a-zA-Z0-9 :?\(\)/]{23})(.+)! ) {
if ( exists( $information->{$1} ) ) {
$self->gw_options( $1, $2 );
}
else {
}
}
elsif ( $line =~ m!^Protein ! ) {
my @high_scores = split( /\s+/, $line );
$self->set_score(@high_scores);
}
else {
}
} } | sub query
{ my ( $self, $arg ) = @_;
if ( defined($arg) ) {
throw(
"Genomic sequence input is not a Bio::SeqI or Bio::Seq or Bio::PrimarySeqI"
)
unless ( $arg->isa("Bio::SeqI")
|| $arg->isa("Bio::Seq")
|| $arg->isa("Bio::PrimarySeqI") );
$self->{'_query'} = $arg;
}
return $self->{'_query'};} | sub run
{ my ( $self, $dir ) = @_;
$self->set_environment;
$self->_align_protein($dir); } | sub set_environment
{ my ($self) = @_;
if ( !-d $ENV{WISECONFIGDIR} ) {
throw( "No WISECONFIGDIR [" . $ENV{WISECONFIGDIR} . "]" );
}} | sub set_score
{ my ( $self, @line ) = @_;
$self->{'_scores'}->{ $line[1] }->{ $line[3] } = $line[5];} | sub valid_options
{ return $options;
} } | sub write_fasta
{ my ( $self, $genfile ) = @_;
my $genio = Bio::SeqIO->new(
'-file' => ">$genfile",
'-format' => 'fasta'
);
$genio->write_seq( $self->query );
$genio = undef; } | General documentation
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Arg [1] : varies
Function : set a varible to a particular value
Returntype: the variable
Exceptions: some throw if not passed the correct arguement
Caller :
Example :