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Coordinates of sub SeqFeatures
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Florent Angly  
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 More options Mar 5 2012, 6:18 pm
From: Florent Angly <florent.an...@gmail.com>
Date: Tue, 06 Mar 2012 09:18:17 +1000
Local: Mon, Mar 5 2012 6:18 pm
Subject: [Bioperl-l] Coordinates of sub SeqFeatures
Hi all,

Could anyone provide clarifications regarding the coordinates of sub
SeqFeatures?
Consider this script, that has a sequence with a feature, which itself
contains a (sub) seqfeature:

Here, I gave the sub SeqFeature coordinates relative to the feature it
is attached to, i.e. position 1..6 of the SeqFeature. However, I get the
exception "Bio::SeqFeature::Generic=HASH(0x15fa150) is not contained
within parent feature, and expansion is not valid". Now, if I provide
the sub SeqFeature coordinates relative to the sequence instead of the
feature it is attached to, i.e. 21..26, everything goes well. Obviously,
add_SeqFeature expects coordinates to be relative to the sequence.

All the documentation I have looked at does not talk about what the
coordinates are relative too. The problem to me is that this seems
counter-intuitive to not being able to provide coordinates relative to
the object a feature is attached too.

Can anyone clarify how the coordinate system for features and sub
features is intended to work?

Thanks,

Florent

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