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Changes in the genic interaction definition #3

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80a6ef3
ajouté un diese
flegeai Feb 16, 2015
0db1c1e
Corrected the status of the Genic interaction and change same strand and
flegeai Feb 16, 2015
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248 changes: 89 additions & 159 deletions FEELnc_v0.1/lib/Bio/SeqFeature/Genic.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -48,7 +48,7 @@ sub new {
$pkg->SUPER::new(
_type => 1,
_distance => 0,
_nested => undef,
_status => undef,
_subtype => undef,
@_,
);
Expand Down Expand Up @@ -78,10 +78,12 @@ sub subtype{
sub _set_subtype(){
my $self = shift;
my $sub_t = shift;
my %subtypes =( 1 => 'exonic', 2=>' intronic', 3 => 'overlapping');
my %subtypes =('exonic' => 1 ,'intronic' => 1, 'none'=> 1);
if (defined($subtypes{$sub_t})){
$self->{'_subtype'} = $sub_t;

}
else {
croak("Error unrecognized subtype : $sub_t\n");
}
}

Expand All @@ -91,37 +93,11 @@ sub _set_subtype(){
sub _get_subtype{
my $self = shift;
if ( _isDefined ($self->{'_subtype'}) == 0) { #undef

$self->_set_subtype($self->_calculate_subtype());
}
return $self->{'_subtype'};
}
=head1 isOverlapping()

Bio::SeqFeature::Interaction

=head1 DESCRIPTION

if it's not intronic and not exonic it's overlapping
see classification rules (T.Derrien)

=cut

sub isOverlapping{

my $interaction = shift;
if ($interaction->_isComplete() == 0) {

croak ("To look if your interaction is Overlapping, you must have an complete interaction \n");
}
if(_isDefined($interaction->{'_subtype'})==0) {
$interaction->_set_subtype($interaction->_calculate_subtype()); # what is the subtype?
}
if($interaction->_get_subtype()==3){
return 1;
}else {return 0;}

}

=head1 calculate_subtype()

Expand All @@ -136,17 +112,16 @@ see classification rules (T.Derrien)

sub _calculate_subtype(){
my $interaction = shift;
if ($interaction->_isComplete() == 0) {

if ($interaction->_isComplete() == 0) {
croak ("To make operation on interaction, you must have an complete interaction \n");
}

if (isExonic($interaction)){

return 1;
return 'exonic';
}elsif ( isIntronic($interaction)){
return 2;
return 'intronic';
}else{
return 3; #overlapping
return 'none'; #overlapping
}
}

Expand All @@ -166,7 +141,7 @@ sub isExonic{
my $interaction = shift;
if ($interaction->_isComplete() == 0) {

croak ("To look if your interaction is Exonic, you must have an complete interaction \n");
croak ("To look if your interaction is Exonic, you must have a complete interaction \n");
}
my $object = $interaction->object();
my $subject = $interaction->subject();
Expand Down Expand Up @@ -196,24 +171,38 @@ sub isIntronic {
#my $pkg = shift;
my $interaction = shift;
if ($interaction->_isComplete() == 0) {

croak ("To look if your interaction is Intronic, you must have an complete interaction \n");
}
my $object = $interaction->object();
my $subject = $interaction->subject();

my $lncrna = $interaction->object();
#print STDERR $lncrna->get_tag_values("transcript_id"), " start: ", $lncrna->start(), " end: ", $lncrna->end(), "\n";
my $mrna = $interaction->subject();

my @introns_mRNA= _getIntrons($mrna);


#print "intronic call \n";
if (scalar(@introns_mRNA) == 0) {return 0}

return (_is_included($lncrna, \@introns_mRNA));
}

my @introns_mRNA= _getIntrons($object);
my @exons_lncRNA = _getExons($subject);

#print "intronic call \n";
# _is_included : private method
# it returns true if the first argument is included into at least one of the following arguments

sub _is_included {
my $first = shift;
my $others = shift;

if (_overlaps_btwn_feature_array(\@exons_lncRNA, \@introns_mRNA, 1) == 1){
return 1;
}else{
return 0;
foreach my $other (@{$others}) {
if ($other->contains($first)) {return(1)}
}

return (0);
}


#_overlaps_btwn_feature_array : private method
# function : say if there is an overlap between the exons of 2 features
# ---------------------------------------------------- -------------------------#
Expand Down Expand Up @@ -346,48 +335,13 @@ sub _getExons {
# ---------------------------------------------------- #

sub _order_array_features {

my @fs_array = @_; #features array
my @f_array = shuffle @fs_array;
my $i = 0;
my %hash=();
#print "taille array : ", $#f_array, "\n";
for ($i =0 ; $i<=$#f_array; $i++){
$hash{$i} = $f_array[$i]->start();

}

my @keys = sort { $hash{$a} <=> $hash{$b} } keys %hash; # sort the hash table on values
$i = 0;
foreach my $cle (@keys) {
$fs_array[$i] = $f_array[$cle]; # cle : indice of the array

$i++;
}
return (@fs_array);
my @ordered_array = sort {$a->start() <=> $b->start()} @fs_array;


return (@ordered_array);
}
# ---------------------------------------------------- #
# printer #

# ---------------------------------------------------- #
=head1 printer()

=head1 DESCRIPTION

$interaction->printer()
print interaction informations

=cut
# this fonction use the SUPER printer and is also defined in intergenic
# sub printer {
# my $self = shift;
# $self->SUPER::printer();
# print "\t Other info \n";
# Bio::SeqFeature::Genic->_ligne_carre();
# print "\t Nested : ",$self->nested(),"\n";
# print "\t Subtype : ",_print_subtype($self->subtype()),"\n";
#
# }


=head1 printer_mini()
Expand All @@ -405,110 +359,86 @@ sub printer_mini {
my $best=shift;
$self->SUPER::printer_mini($best);

my $status = 'not_nested';
if ($self->nested==1) {
$status='nested';
}
print "\t Status=",$status;
print "\t Subtype=",_print_subtype($self->subtype()),"\n";
print "\t Status=",$self->status();
print "\t Subtype=", $self->subtype(),"\n";

}

=head1 DESCRIPTION

$interaction->printer()
print interaction informations

=cut
# this fonction use the SUPER printer and is also defined in intergenic
sub printer {
my $self = shift;
$self->SUPER::printer();
print "\t Other info \n";
Bio::SeqFeature::Genic->_ligne_carre();
print "\t Nested : ",$self->nested(),"\n";
print "\t Subtype : ",_print_subtype($self->subtype()),"\n";

}
# ---------------------------------------------------- #
# ---------------------------------------------------- #
#_print_subtype : private method
# function : do the correspondance between the subtype number and the string corresponding

sub _print_subtype{
my $subtype = shift;
my %subtypes =( 1 => 'exonic', 2=>' intronic', 3 => 'containing');
if (exists $subtypes{$subtype}) {
return $subtypes{$subtype};
}
return $subtype;
}
# ---------------------------------------------------- #
# ---------------------------------------------------- #
=head1 nested()
=head1 status()

Bio::SeqFeature::Generic

=head1 DESCRIPTION

my $nested = $interaction->nested()
my $status = $interaction->status()

say if the interaction is nested or not (see classification rules Derrien et al 2011)
says what is the interaction status (containing, nested or overlapping) or not (see classification rules Derrien et al 2011)
=cut

sub nested {
sub status {
my $self =shift;
my $nested = $self->_get_nested();
return $nested;
my $status = $self->_get_status();
return $status;
}
# ---------------------------------------------------- #
# ---------------------------------------------------- #
#_get_nested : private method
# function : getter of nested attribute
sub _get_nested{


#_get_status : private method
# function : getter of status attribute

sub _get_status{
my $self = shift;
if ( _isDefined($self->{"_nested"}) == 0 ){
$self->_set_nested($self->_isNested());
if ( _isDefined($self->{"_status"}) == 0 ){
$self->_set_status($self->_calculate_status());
}
return $self->{'_nested'};
return $self->{'_status'};
}
# ---------------------------------------------------- #
# ---------------------------------------------------- #

#_set_nested : private method
# function : setter of nested attribute
sub _set_nested{

#_set_status : private method
# function : setter of status attribute


sub _set_status{
my $self = shift;
if (@_) {
$self->{'_nested'} = shift;
}else {
croak ("Nested undefined, cannot set nested \n"); # i want it to die because it's a protected method; then the developper make an error
if (@_) {
my $status = shift;
my %status =('nested' => 1 ,'containing' => 1, 'overlapping'=> 1);
unless (exists $status{$status}) {
croak("Error unrecognized status : $status\n");
}
$self->{'_status'} = $status;
}
else {
croak ("type undefined, cannot set \n"); # i want it to die because it's a protected method; then the developper make an error
}
}

# ---------------------------------------------------- #
# ---------------------------------------------------- #
# isNested : private method
# function : say if nested or not

sub _isNested{

# calculate_status : private method
# function : returns the status of the interaction (nested, containing or overlapping)

sub _calculate_status{
my $self = shift;

if ($self->_isComplete() == 0) {
croak ("To look if your interaction is Nested, you must have an complete interaction \n");
croak ("To get the status of your interaction, you must have a complete interaction \n");
}
my $object = $self->object();
my $subject = $self->subject();

my $lncrna = $self->object();
my $mrna = $self->subject();

if ($object->contains($subject)){

return 1;
} else{

return 0;
}
if ($lncrna->contains($mrna)) {
return 'containing';
}


if ($mrna->contains($lncrna)){
return ('nested');
}

return 'overlapping';
}


Expand Down
2 changes: 1 addition & 1 deletion FEELnc_v0.1/lib/Bio/SeqFeature/Interaction.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -500,7 +500,7 @@ sub _print_finfo{
# 1 <=> anti direction
sub _conversion_direction {
my $i= shift;
my %direction = ("1","same strand","-1","different strand","0","strand(s) unknow");
my %direction = ("1","sense","-1","antisense","0","strand(s) unknow");
if (exists $direction{$i} ) {
return ($direction{$i});
}else{ return "$i unknow direction";}
Expand Down
2 changes: 1 addition & 1 deletion FEELnc_v0.1/lib/Bio/SeqFeature/LncRNAs_Factory.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -219,7 +219,7 @@ sub DoItForMe{
print "#lncRNA file : lncrna : $lncrna_file \n";
print "#mRNA file : $mrna_file\n";
print "#Minimal window size : $window\n";
print "Maximal window size : $max_window\n";
print "#Maximal window size : $max_window\n";
print "#Number of lncRNA : $numberlnc \n";
print "#Number of mRNA : $nb_mrna\n";
print "#Number of interaction : $nombre \n";
Expand Down