1.

How Do I Parse The Cds Join Or Complement Statements In Genbank Or Embl Files To Get The Sub-locations?

Answer»

For example, how can I GET the the COORDINATES 45 and 122 in join(45..122,233..267) :
You could use primary_tag to FIND the CDS features and the Bio::LOCATION::SplitLocationI object to get the coordinates:
foreach my $feature ($seqobj->top_SeqFeatures){
if ( $feature->location->isa('Bio::Location::SplitLocationI') and $feature->primary_tag EQ 'CDS' ) {
foreach my $location ( $feature->location->sub_Location ) {
print $location->start , ".." , $location->end, "n";
}
}
}

For example, how can I get the the coordinates 45 and 122 in join(45..122,233..267) :
You could use primary_tag to find the CDS features and the Bio::Location::SplitLocationI object to get the coordinates:
foreach my $feature ($seqobj->top_SeqFeatures){
if ( $feature->location->isa('Bio::Location::SplitLocationI') and $feature->primary_tag eq 'CDS' ) {
foreach my $location ( $feature->location->sub_Location ) {
print $location->start , ".." , $location->end, "n";
}
}
}


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