Genome insertion trigers recalculate CDS on non-coding features about apollo

[childers]

Oops, left out the insertion:

Scaffold1   WebApollo   insertion   875615  875615  .   +   .   Name=024CEEAB2AE0C4F9AE1490815C67FDC3;

##FASTA
>024CEEAB2AE0C4F9AE1490815C67FDC3
AAAAAAAAAAAAAAAAACCCCCCCCC

[monicacecilia]

@nathandunn Expected output should be "same as above", not a non-coding feature (tRNA in this case) with CDSs.

[nathandunn]

Interesting, when you delete the insertion, everything else stays.

Also, if the insertion precedes the annotation you don't get the extra CDS calculations.

[monicacecilia]

just fyi -- and I haven't looked to see if it applies here -- current, sequence alterations cannot overlap each other.

On Nov 26, 2014, at 1:50 PM, Nathan Dunn [email protected] wrote:

Interesting, when you delete the insertion, everything else stays.

Also, if the insertion precedes the annotation you don't get the extra CDS calculations.

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[nathandunn]

@monicacecilia Do we only want to calculate for "mRNA" transcripts, or other ones, as well?

[nathandunn]

@monicacecilia It is calculating the CDS when setting the longest ORF. I am telling it to do this only if it is a transcript of type mRNA. Not sure if snRNA, miRNA, etc. should also be included. . . for calculating or if we should exclude tRNA, ncRNA, etc.

[selewis]

yes, also exclude tRNA (any kind of ncRNA in other words). Only protein
coding should have the protein coding calculated.

p.s. it would be difficult to allow genomic sequence alterations to overlap
because then we'd have to know the order with which to apply the
alterations. However when/if we reuse this code for indicating natural
variation/alterations we'll need to allow overlaps coming from different
individuals, even if the alterations for each individual are
non-overlapping... (need to draw a picture)

-S

On Wed, Nov 26, 2014 at 2:08 PM, Nathan Dunn [email protected]
wrote:

@monicacecilia https://github.com/monicacecilia It is calculating the
CDS when setting the longest ORF. I am telling it to do this only if it is
a transcript of type mRNA. Not sure if snRNA, miRNA, etc. should also be
included. . . for calculating or if we should exclude tRNA, ncRNA, etc.

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#30 (comment).

[nathandunn]

@cmdcolin @childers Sorry, I should have fixed this during the break as it was failing the regression tests. The original code was correct, we want to calculate the CDS if a coding transcript. The original fix should do this. I just need to create a test that handles both cases. Unfortunately the default is "transcript", which should not be encoding.

[selewis]

to be finicky

"transcript" is not necessarily encoding.

if it is a transcript of type mRNA (a subclass of transcript in SO) then it
is an encoding transcript.

the transcripts of protein coding genes should properly be typed using the
sub-class mRNA

On Mon, Dec 1, 2014 at 8:50 AM, Nathan Dunn [email protected]
wrote:

@cmdcolin https://github.com/cmdcolin @childers
https://github.com/childers Sorry, I should have fixed this during the
break as it was failing the regression tests. The original code was
correct, we want to calculate the CDS if a coding transcript. The original
fix should do this. I just need to create a test that handles both
cases. Unfortunately the default is "transcript", which should not be
encoding.

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#30 (comment).

[nathandunn]

You are exactly correct. “Transcript” is actually used with pseudogenes and MRNA (at least in our current system) has no sub-classess.

I’m pretty sure this implementation is correct, but I will need others to test. Once I get the rest of the 1.0.3 bugs sorted out, I’ll put it up for testing.

Nathan

On Dec 1, 2014, at 11:02 AM, selewis [email protected] wrote:

to be finicky

"transcript" is not necessarily encoding.

if it is a transcript of type mRNA (a subclass of transcript in SO) then it
is an encoding transcript.

the transcripts of protein coding genes should properly be typed using the
sub-class mRNA

On Mon, Dec 1, 2014 at 8:50 AM, Nathan Dunn [email protected]
wrote:

@cmdcolin https://github.com/cmdcolin @childers
https://github.com/childers Sorry, I should have fixed this during the
break as it was failing the regression tests. The original code was
correct, we want to calculate the CDS if a coding transcript. The original
fix should do this. I just need to create a test that handles both
cases. Unfortunately the default is "transcript", which should not be
encoding.

—
Reply to this email directly or view it on GitHub
#30 (comment).

—
Reply to this email directly or view it on GitHub #30 (comment).

[monicacecilia]

works now. Thanks!

[nathandunn]

@monicacecilia I want to retest this in 2.0.0 I looked and it appears that we have the correct code in there, but I want some separate eyes to verify.

[monicacecilia]

@nathandunn You are correct, genomic insertions are no longer causing the generation of a CDS in tRNA features. However, while investigating this issue, I found a few other things. Please see #263

[nathandunn]

@deepakunni3 Could this be relevant?

[deepakunni3]

@nathandunn This bug doesn't occur in Apollo 2.0

The rationale holds for recalculating CDS only when the transcript is an instance of mRNA.