Re: EST_match for unigenes

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Re: EST_match for unigenes

Stephen Ficklin-2
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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Re: EST_match for unigenes

Stephen Ficklin-2
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,
>>
>>
>



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Re: EST_match for unigenes

Tony Power
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,
>>>
>>>
>>
>
>

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Re: EST_match for unigenes

Lacey-Anne Sanderson
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
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,






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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/
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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/
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