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Hello Duarte,<br>
<br>
Let's address the first pair, get_all_Introns and
get_all_CDS_Introns. The documentation for get_all_CDS_Introns says:<br>
Returns an listref of the introns between coding exons in this
transcript in order<br>
<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
<div class="moz-cite-prefix">On 13/09/16 12:27, Duarte Molha wrote:<br>
</div>
<blockquote
cite="mid:CAGqkoELzyTLGb4c6LgwTjaM6cFjsqdyMPcOpRH5oaspaFSW19Q@mail.gmail.com"
type="cite">
<div dir="ltr">Dear Devs
<div><br>
</div>
<div>I was browsing through the API documentation and became a
bit confused with some of the methods</div>
<div><br>
</div>
<div>in the Transcript object, there is 2 methods wich to my
mind mean the same thing</div>
<div><br>
</div>
<div>That exactly is the difference between </div>
<div><br>
</div>
<div>get_all_Introns</div>
<div>and</div>
<div>get_all_CDS_Introns</div>
<div><br>
</div>
<div><br>
</div>
<div>or </div>
<div><br>
</div>
<div>get_all_Exons</div>
<div>and</div>
<div>get_all_Exon_Transcripts</div>
<div><br>
</div>
<div>Many thanks</div>
<div><br>
Duarte</div>
<div><br>
</div>
<div>
</div>
</div>
<br>
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<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Matthew Laird - Ensembl Core Developer
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-494274
Fax: +44-(0)1223-494468
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