[ensembl-dev] get_all_introns or get_all_CDS_introns

[Matthew Laird]

Hello Duarte,

Let's address the first pair, get_all_Introns and get_all_CDS_Introns. 
The documentation for get_all_CDS_Introns says:
Returns an listref of the introns between coding exons in this 
transcript in order

As in, not the introns which might be between non-coding exons (UTR 
regions). get_all_Introns will return all introns, between coding exons 
or not.

Next get_all_Exons and get_all_Exon_Transcripts, in the documentation 
for get_all_ExonTranscripts it lists the return type as a list of 
Bio::EnsEMBL::ExonTranscript and get_all_Exons returns a list of 
Bio::EnsEMBL::Exon. An Bio::EnsEMBL::Exon object is not associated with 
a transcript, you can't call transcript() on it, it could be shared 
among multiple transcripts. A Bio::EnsEMBL::ExonTranscript is designed 
for when you need to be able to link back up to a transcript when 
operating on exons, it has a specific transcript associated with it.

The first pair are quite different in what they do. The second pair, for 
most basic usage patterns of users (get a transcript, cycle through the 
exons), are likely more interchangeable, but we'd recommend using the 
former of those two, it's a bit more refined. The latter is more used in 
our internal dumping pipelines and isn't as feature complete.

On 13/09/16 12:27, Duarte Molha wrote:
> Dear Devs
>
> I was browsing through the API documentation and became a bit confused 
> with some of the methods
>
> in the Transcript object, there is 2 methods wich to my mind mean the 
> same thing
>
> That exactly is the difference between
>
> get_all_Introns
> and
> get_all_CDS_Introns
>
>
> or
>
> get_all_Exons
> and
> get_all_Exon_Transcripts
>
> Many thanks
>
> Duarte
>
>
>
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-- 
Matthew Laird - Ensembl Core Developer
The European Bioinformatics Institute (EMBL-EBI)
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