Bio::LiveSeq Gene
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Summary
Bio::LiveSeq::Gene - Range abstract class for LiveSeq
Package variables
No package variables defined.
Included modules
Bio::LiveSeq::Prim_Transcript
Carp
Synopsis
  # documentation needed
Description
This is used as storage for all object references concerning a particular gene.
Methods
newDescriptionCode
_set_Gene_in_all
No description
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name
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features
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get_DNA
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get_Transcripts
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get_Translations
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get_Prim_Transcripts
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get_Repeat_Units
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get_Repeat_Regions
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get_Introns
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get_Exons
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featuresnum
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upbound
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downbound
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printfeaturesnum
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maxtranscript
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delete_Obj
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verboseDescriptionCode
warn
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Methods description
newcode    nextTop
  Title   : new
Usage : $gene = Bio::LiveSeq::Gene->new(-name => "name",
-features => $hashref
-upbound => $min
-downbound => $max);
Function: generates a new Bio::LiveSeq::Gene Returns : reference to a new object of class Gene Errorcode -1 Args : one string and one hashreference containing all features defined for the Gene and the references to the LiveSeq objects for those features. Two labels for defining boundaries of the gene. Usually the boundaries will reflect max span of transcript, exon... features, while the DNA sequence will be created with some flanking regions (e.g. with the EMBL_SRS::gene2liveseq routine). If these two labels are not given, they will default to the start and end of the DNA object. Note : the format of the hash has to be like DNA => reference to LiveSeq::DNA object Transcripts => reference to array of transcripts objrefs Transclations => reference to array of transcripts objrefs Exons => .... Introns => .... Prim_Transcripts => .... Repeat_Units => .... Repeat_Regions => .... Only DNA and Transcripts are mandatory
verbosecodeprevnextTop
 Title   : verbose
Usage : $self->verbose(0)
Function: Sets verbose level for how ->warn behaves
-1 = silent: no warning
0 = reduced: minimal warnings
1 = default: all warnings
2 = extended: all warnings + stack trace dump
3 = paranoid: a warning becomes a throw and the program dies
Note: a quick way to set all LiveSeq objects at the same verbosity level is to change the DNA level object, since they all look to that one if their verbosity_level attribute is not set. But the method offers fine tuning possibility by changing the verbose level of each object in a different way. So for example, after $loader= and $gene= have been retrieved by a program, the command $gene->verbose(0); would set the default verbosity level to 0 for all objects. Returns : the current verbosity level Args : -1,0,1,2 or 3
Methods code
newdescriptionprevnextTop
sub new {
  my ($thing, %args) = @_;
  my $class = ref($thing) || $thing;
  my ($i,$self,%gene);

  my ($name,$inputfeatures,$upbound,$downbound)=($args{-name},$args{-features},$args{-upbound},$args{-downbound});

  unless (ref($inputfeatures) eq "HASH") {
    carp "$class not initialised because features hash not given";
    return (-1);
  }

  my %features=%{$inputfeatures}; # this is done to make our own hash&ref, not
my $features=\%features; # the ones input'ed, that could get destroyed
my $DNA=$features->{'DNA'}; unless (ref($DNA) eq "Bio::LiveSeq::DNA") { carp "$class not initialised because DNA feature not found"; return (-1); } my ($minstart,$maxend);# used to calculate Gene->maxtranscript from Exon, Transcript (CDS) and Prim_Transcript features
my ($start,$end); my @Transcripts=@{$features->{'Transcripts'}}; my $strand; unless (ref($Transcripts[0]) eq "Bio::LiveSeq::Transcript") { $self->warn("$class not initialised: first Transcript not a LiveSeq object"); return (-1); } else { $strand=$Transcripts[0]->strand; # for maxtranscript consistency check
} for $i (@Transcripts) { ($start,$end)=($i->start,$i->end); unless ((ref($i) eq "Bio::LiveSeq::Transcript")&&($DNA->valid($start))&&($DNA->valid($end))) { $self->warn("$class not initialised because of problems in Transcripts feature"); return (-1); } else { } unless($minstart) { $minstart=$start; } # initialize
unless($maxend) { $maxend=$end; } # initialize
if ($i->strand != $strand) { $self->warn("$class not initialised because exon-CDS-prim_transcript features do not share the same strand!"); return (-1); } if (($strand == 1)&&($start < $minstart)||($strand == -1)&&($start > $minstart)) { $minstart=$start; } if (($strand == 1)&&($end > $maxend)||($strand == -1)&&($end < $maxend)) { $maxend=$end; } } my @Translations; my @Introns; my @Repeat_Units; my @Repeat_Regions; my @Prim_Transcripts; my @Exons; if (defined($features->{'Translations'})) { @Translations=@{$features->{'Translations'}}; } if (defined($features->{'Exons'})) { @Exons=@{$features->{'Exons'}}; } if (defined($features->{'Introns'})) { @Introns=@{$features->{'Introns'}}; } if (defined($features->{'Repeat_Units'})) { @Repeat_Units=@{$features->{'Repeat_Units'}}; } if (defined($features->{'Repeat_Regions'})) { @Repeat_Regions=@{$features->{'Repeat_Regions'}}; } if (defined($features->{'Prim_Transcripts'})) { @Prim_Transcripts=@{$features->{'Prim_Transcripts'}}; } if (@Translations) { for $i (@Translations) { ($start,$end)=($i->start,$i->end); unless ((ref($i) eq "Bio::LiveSeq::Translation")&&($DNA->valid($start))&&($DNA->valid($end))) { $self->warn("$class not initialised because of problems in Translations feature"); return (-1); } } } if (@Exons) { for $i (@Exons) { ($start,$end)=($i->start,$i->end); unless ((ref($i) eq "Bio::LiveSeq::Exon")&&($DNA->valid($start))&&($DNA->valid($end))) { $self->warn("$class not initialised because of problems in Exons feature"); return (-1); } if ($i->strand != $strand) { $self->warn("$class not initialised because exon-CDS-prim_transcript features do not share the same strand!"); return (-1); } if (($strand == 1)&&($start < $minstart)||($strand == -1)&&($start > $minstart)) { $minstart=$start; } if (($strand == 1)&&($end > $maxend)||($strand == -1)&&($end < $maxend)) { $maxend=$end; } } } if (@Introns) { for $i (@Introns) { ($start,$end)=($i->start,$i->end); unless ((ref($i) eq "Bio::LiveSeq::Intron")&&($DNA->valid($start))&&($DNA->valid($end))) { $self->warn("$class not initialised because of problems in Introns feature"); return (-1); } } } if (@Repeat_Units) { for $i (@Repeat_Units) { ($start,$end)=($i->start,$i->end); unless ((ref($i) eq "Bio::LiveSeq::Repeat_Unit")&&($DNA->valid($start))&&($DNA->valid($end))) { $self->warn("$class not initialised because of problems in Repeat_Units feature"); return (-1); } } } if (@Repeat_Regions) { for $i (@Repeat_Regions) { ($start,$end)=($i->start,$i->end); unless ((ref($i) eq "Bio::LiveSeq::Repeat_Region")&&($DNA->valid($start))&&($DNA->valid($end))) { $self->warn("$class not initialised because of problems in Repeat_Regions feature"); return (-1); } } } if (@Prim_Transcripts) { for $i (@Prim_Transcripts) { ($start,$end)=($i->start,$i->end); unless ((ref($i) eq "Bio::LiveSeq::Prim_Transcript")&&($DNA->valid($start))&&($DNA->valid($end))) { $self->warn("$class not initialised because of problems in Prim_Transcripts feature"); return (-1); } if ($i->strand != $strand) { $self->warn("$class not initialised because exon-CDS-prim_transcript features do not share the same strand!"); return (-1); } if (($strand == 1)&&($start < $minstart)||($strand == -1)&&($start > $minstart)) { $minstart=$start; } if (($strand == 1)&&($end > $maxend)||($strand == -1)&&($end < $maxend)) { $maxend=$end; } } } # create an array containing all obj references for all Gene Features
# useful for _set_Gene_in_all
my @allfeatures; push (@allfeatures,$DNA,@Transcripts,@Translations,@Exons,@Introns,@Repeat_Units,@Repeat_Regions,@Prim_Transcripts); # create hash holding numbers for Gene Features
my %multiplicity; my $key; my @array; foreach $key (keys(%features)) { unless ($key eq "DNA") { @array=@{$features{$key}}; $multiplicity{$key}=scalar(@array); } } $multiplicity{DNA}=1; # create maxtranscript object. It's a Prim_Transcript with start as the
# minimum start and end as the maximum end.
# usually these start and end will be the same as the gene->upbound and
# gene->downbound, but maybe there could be cases when this will be false
# (e.g. with repeat_units just before the prim_transcript or first exon,
# but still labelled with the same /gene qualifier)
my $maxtranscript=Bio::LiveSeq::Prim_Transcript->new(-start => $minstart, -end => $maxend, -strand => $strand, -seq => $DNA); # check the upbound downbound parameters
if (defined($upbound)) { unless ($DNA->valid($upbound)) { $self->warn("$class not initialised because upbound label not valid"); return (-1); } } else { $upbound=$DNA->start; } if (defined($downbound)) { unless ($DNA->valid($downbound)) { $self->warn("$class not initialised because downbound label not valid"); return (-1); } } else { $downbound=$DNA->end; } %gene = (name => $name, features => $features,multiplicity =>\% multiplicity, upbound => $upbound, downbound => $downbound, allfeatures =>\@ allfeatures, maxtranscript => $maxtranscript); $self =\% gene; $self = bless $self, $class; _set_Gene_in_all($self,@allfeatures); return $self; } # this sets the "gene" objref in all the objects "belonging" to the Gene,
# i.e. in all its Features.
}
_set_Gene_in_alldescriptionprevnextTop
sub _set_Gene_in_all {
  my $Gene=shift;
  my $self;
  foreach $self (@_) {
    $self->gene($Gene);
  }
}

# you can get or set the name of the gene
}
namedescriptionprevnextTop
sub name {
  my ($self,$value) = @_;
  if (defined $value) {
    $self->{'name'} = $value;
  }
  unless (exists $self->{'name'}) {
    return "unknown";
  } else {
    return $self->{'name'};
  }
}

# gets the features hash
}
featuresdescriptionprevnextTop
sub features {
  my $self=shift;
  return ($self->{'features'});
}
get_DNAdescriptionprevnextTop
sub get_DNA {
  my $self=shift;
  return ($self->{'features'}->{'DNA'});
}
get_TranscriptsdescriptionprevnextTop
sub get_Transcripts {
  my $self=shift;
  return ($self->{'features'}->{'Transcripts'});
}
get_TranslationsdescriptionprevnextTop
sub get_Translations {
  my $self=shift;
  return ($self->{'features'}->{'Translations'});
}
get_Prim_TranscriptsdescriptionprevnextTop
sub get_Prim_Transcripts {
  my $self=shift;
  return ($self->{'features'}->{'Prim_Transcripts'});
}
get_Repeat_UnitsdescriptionprevnextTop
sub get_Repeat_Units {
  my $self=shift;
  return ($self->{'features'}->{'Repeat_Units'});
}
get_Repeat_RegionsdescriptionprevnextTop
sub get_Repeat_Regions {
  my $self=shift;
  return ($self->{'features'}->{'Repeat_Regions'});
}
get_IntronsdescriptionprevnextTop
sub get_Introns {
  my $self=shift;
  return ($self->{'features'}->{'Introns'});
}
get_ExonsdescriptionprevnextTop
sub get_Exons {
  my $self=shift;
  return ($self->{'features'}->{'Exons'});
}
featuresnumdescriptionprevnextTop
sub featuresnum {
  my $self=shift;
  return ($self->{'multiplicity'});
}
upbounddescriptionprevnextTop
sub upbound {
  my $self=shift;
  return ($self->{'upbound'});
}
downbounddescriptionprevnextTop
sub downbound {
  my $self=shift;
  return ($self->{'downbound'});
}
printfeaturesnumdescriptionprevnextTop
sub printfeaturesnum {
  my $self=shift;
  my ($key,$value);
  my %hash=%{$self->featuresnum};
  foreach $key (keys(%hash)) {
    $value=$hash{$key};
    print "\t$key => $value\n";
  }
}
maxtranscriptdescriptionprevnextTop
sub maxtranscript {
  my $self=shift;
  return ($self->{'maxtranscript'});
}
delete_ObjdescriptionprevnextTop
sub delete_Obj {
  my $self = shift;
  my @values= values %{$self};
  my @keys= keys %{$self};

  foreach my $key ( @keys ) {
    delete $self->{$key};
  }
  foreach my $value ( @values ) {
    if (index(ref($value),"LiveSeq") != -1) { # object case
eval { # delete $self->{$value};
$value->delete_Obj; }; } elsif (index(ref($value),"ARRAY") != -1) { # array case
my @array=@{$value}; my $element; foreach $element (@array) { eval { $element->delete_Obj; }; } } elsif (index(ref($value),"HASH") != -1) { # object case
my %hash=%{$value}; my $element; foreach $element (%hash) { eval { $element->delete_Obj; }; } } } return(1);
}
verbosedescriptionprevnextTop
sub verbose {
  my $self=shift;
  my $value = shift;
  return $self->{'features'}->{'DNA'}->verbose($value);
}
warndescriptionprevnextTop
sub warn {
  my $self=shift;
  my $value = shift;
  return $self->{'features'}->{'DNA'}->warn($value);
}



1;
}
General documentation
AUTHOR - Joseph A.L. InsanaTop
Email: Insana@ebi.ac.uk, jinsana@gmx.net
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _