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Re: EST_match for unigenes

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Stephen Ficklin-2

Re: EST_match for unigenes

Hi Tony,

Good morning. I'm CC'ing the list as your question about the EST_match
may be helpful for others. The behavior you describe is correct for the
way the alignments are stored. ESTs are aligned to contigs via an
'EST_match' feature in your GFF file. This is because an EST does not
always overlap completely with the contig depending on the software used
to do the assembly--only portions of ESTs may align. Therefore we use
an EST_match feature for the alignment. See here for an example:
http://gmod.org/wiki/GFF#Alignments

EST --> EST_match <-- Contig

In reality you don't want the site visitors to see the EST_match
features. But by default Tripal treats all features the same. It
doesn't know the difference between a gene, mRNA, contig, EST,
EST_match, etc. So that is why you have links to EST_matches on your
contig alignments page rather than links to ESTs. So, to get links to
your ESTs on your contig page and to bypass the EST_match feature you
need to edit the
sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
to handle that special case. I believe however that I can make that
adjustment in the template for you in the development code. When it's
ready I'll let you know.

Stephen

On 7/10/2012 5:45 AM, Tony Power wrote:

> Hi again Stephen,
>
> I noticed some strange behavior on the site.
>
> For instance:
> 1-Select the first contig and then select "Alignments".
> 2-Now select the first EST_match.
> 3-Now "EST_match Sequence" -> No sequence is shown;
>
> 4-Now select "Alignments" (of that EST_match).
> 5-From the alignments select the EST_match that it aligns to.
> 6-Select "EST_match Sequence" -> The sequence is shown.
>
> What might be the problem?
>
> Obrigado,
>
>

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Stephen Ficklin-2

Re: EST_match for unigenes

Hi Tony,

If you get the most recent version of the tripal_theme 6.x-1.x branch
from the development git repository it now contains an update that
resolves the issue with the EST_match that you are having. Let me know
if it works for you.

http://drupal.org/node/1342972/git-instructions/6.x-1.x

Stephen

On 7/10/2012 9:26 AM, Stephen Ficklin wrote:

> Hi Tony,
>
> Good morning. I'm CC'ing the list as your question about the
> EST_match may be helpful for others. The behavior you describe is
> correct for the way the alignments are stored. ESTs are aligned to
> contigs via an 'EST_match' feature in your GFF file. This is because
> an EST does not always overlap completely with the contig depending on
> the software used to do the assembly--only portions of ESTs may
> align. Therefore we use an EST_match feature for the alignment. See
> here for an example: http://gmod.org/wiki/GFF#Alignments
>
> EST --> EST_match <-- Contig
>
> In reality you don't want the site visitors to see the EST_match
> features. But by default Tripal treats all features the same. It
> doesn't know the difference between a gene, mRNA, contig, EST,
> EST_match, etc. So that is why you have links to EST_matches on your
> contig alignments page rather than links to ESTs. So, to get links
> to your ESTs on your contig page and to bypass the EST_match feature
> you need to edit the
> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
> to handle that special case. I believe however that I can make that
> adjustment in the template for you in the development code. When it's
> ready I'll let you know.
>
> Stephen
>
>
> On 7/10/2012 5:45 AM, Tony Power wrote:
>> Hi again Stephen,
>>
>> I noticed some strange behavior on the site.
>>
>> For instance:
>> 1-Select the first contig and then select "Alignments".
>> 2-Now select the first EST_match.
>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>
>> 4-Now select "Alignments" (of that EST_match).
>> 5-From the alignments select the EST_match that it aligns to.
>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>
>> What might be the problem?
>>
>> Obrigado,
>>
>>
>

Tony Power

Re: EST_match for unigenes

Hi Stephen,

Just updated to the new Tripal Theme.
Something is not working properly. To understand what I mean, please,
click on one of the contigs.

Do I also need to update the Tripal module? I just updated the Theme.

Thanks ;)

Tony

On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin <[hidden email]> wrote:

> Hi Tony,
>
> If you get the most recent version of the tripal_theme 6.x-1.x branch from
> the development git repository it now contains an update that resolves the
> issue with the EST_match that you are having. Let me know if it works for
> you.
>
> http://drupal.org/node/1342972/git-instructions/6.x-1.x
>
>
> Stephen
>
>
> On 7/10/2012 9:26 AM, Stephen Ficklin wrote:
>>
>> Hi Tony,
>>
>> Good morning. I'm CC'ing the list as your question about the EST_match
>> may be helpful for others. The behavior you describe is correct for the way
>> the alignments are stored. ESTs are aligned to contigs via an 'EST_match'
>> feature in your GFF file. This is because an EST does not always overlap
>> completely with the contig depending on the software used to do the
>> assembly--only portions of ESTs may align. Therefore we use an EST_match
>> feature for the alignment. See here for an example:
>> http://gmod.org/wiki/GFF#Alignments
>>
>> EST --> EST_match <-- Contig
>>
>> In reality you don't want the site visitors to see the EST_match features.
>> But by default Tripal treats all features the same. It doesn't know the
>> difference between a gene, mRNA, contig, EST, EST_match, etc. So that is
>> why you have links to EST_matches on your contig alignments page rather than
>> links to ESTs. So, to get links to your ESTs on your contig page and to
>> bypass the EST_match feature you need to edit the
>> sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
>> to handle that special case. I believe however that I can make that
>> adjustment in the template for you in the development code. When it's ready
>> I'll let you know.
>>
>> Stephen
>>
>>
>> On 7/10/2012 5:45 AM, Tony Power wrote:
>>>
>>> Hi again Stephen,
>>>
>>> I noticed some strange behavior on the site.
>>>
>>> For instance:
>>> 1-Select the first contig and then select "Alignments".
>>> 2-Now select the first EST_match.
>>> 3-Now "EST_match Sequence" -> No sequence is shown;
>>>
>>> 4-Now select "Alignments" (of that EST_match).
>>> 5-From the alignments select the EST_match that it aligns to.
>>> 6-Select "EST_match Sequence" -> The sequence is shown.
>>>
>>> What might be the problem?
>>>
>>> Obrigado,
>>>
>>>
>>
>
>

Lacey-Anne Sanderson

Re: EST_match for unigenes

Hi Tony,

Yes, the theme and the module are quite closely linked (developed together) so I would suggest always updating the module at the same time as the theme.

~Lacey

------------------------------------------------------

Lacey-Anne Sanderson

Bioinformaticist

Pulse Crop Breeding and Genetics

Phone: (306) 966-4975

Email: [hidden email]

Room 3C06 Agriculture

Department of Plant Sciences

University of Saskatchewan

On 2012-07-16, at 6:58 AM, Tony Power wrote:

Hi Stephen,

Just updated to the new Tripal Theme.
Something is not working properly. To understand what I mean, please,
click on one of the contigs.

Do I also need to update the Tripal module? I just updated the Theme.

Thanks ;)

Tony

On Sat, Jul 14, 2012 at 3:04 AM, Stephen Ficklin <[hidden email]> wrote:
Hi Tony,

If you get the most recent version of the tripal_theme 6.x-1.x branch from
the development git repository it now contains an update that resolves the
issue with the EST_match that you are having. Let me know if it works for
you.

http://drupal.org/node/1342972/git-instructions/6.x-1.x

Stephen

On 7/10/2012 9:26 AM, Stephen Ficklin wrote:

Hi Tony,

Good morning. I'm CC'ing the list as your question about the EST_match
may be helpful for others. The behavior you describe is correct for the way
the alignments are stored.   ESTs are aligned to contigs via an 'EST_match'
feature in your GFF file.   This is because an EST does not always overlap
completely with the contig depending on the software used to do the
assembly--only portions of ESTs may align. Therefore we use an EST_match
feature for the alignment.   See here for an example:
http://gmod.org/wiki/GFF#Alignments

EST --> EST_match <-- Contig

In reality you don't want the site visitors to see the EST_match features.
But by default Tripal treats all features the same. It doesn't know the
difference between a gene, mRNA, contig, EST, EST_match, etc. So that is
why you have links to EST_matches on your contig alignments page rather than
links to ESTs.   So, to get links to your ESTs on your contig page and to
bypass the EST_match feature you need to edit the
sites/all/themes/tripal_theme/tripal_feature/tripal_feature_featurelocs_as_parent.tpl.php
to handle that special case.   I believe however that I can make that
adjustment in the template for you in the development code. When it's ready
I'll let you know.

Stephen

On 7/10/2012 5:45 AM, Tony Power wrote:

Hi again Stephen,

I noticed some strange behavior on the site.

For instance:
1-Select the first contig and then select "Alignments".
2-Now select the first EST_match.
3-Now "EST_match Sequence" -> No sequence is shown;

4-Now select "Alignments" (of that EST_match).
5-From the alignments select the EST_match that it aligns to.
6-Select "EST_match Sequence" -> The sequence is shown.

What might be the problem?

Obrigado,

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-tripal mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal