Hi all,
I would like to start my first contact with Jalview development in deep with a BED parser. I’ve seend BED file format and seems quite easy to parse so I think I can manage on my own with the parsing but my problem is that I don’t where to store parsed information. Any suggestion?
Thanks so much in advance!
David
Hi David.
I would like to start my first contact with Jalview development in deep with a BED parser. I've seend BED file format and seems quite easy to parse so I think I can manage on my own with the parsing but my problem is that I don't where to store parsed information. Any suggestion?
I presume by BED you mean this format:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1
It would be quite useful to be able to parse these kind of files, but since they are designed for UCSC, it isn't as simple as 'implement a tabbed file parser'. BED data files conventionally generate annotation tracks, so you would need to implement a datamodel renderer that generates Jalview style annotation tracks from BED files.
As ever, however, the first thing to do is create a new feature on issues.jalview.org for this, so we can discuss details over there. I've a feeling this might become an EPIC, though, since being able to read and write BED files could be very useful for people who want to publish data to UCSC, or import from UCSC.
This would also make a great Hackathon topic to work on in Oxford on day 2 of the workshop!
Jim.
On 25/11/2013 17:03, David Roldán Martínez wrote:
Jim,
I cannot attend to Oxford workshop, though I would like to. I contribute to Jalview only at my free-time (that’s why my contributions are so tiny) and I have no vacations nor budget to go there. Will it be possible to attend by videoconference? May I send you slides for a session about how to develop i18n-compliant code?
Cheers,
D.
2013/11/26 Jim Procter <jprocter@compbio.dundee.ac.uk>
Hi David.
On 25/11/2013 17:03, David Roldán Martínez wrote:
I would like to start my first contact with Jalview development in
deep with a BED parser. I’ve seend BED file format and seems quite
easy to parse so I think I can manage on my own with the parsing but
my problem is that I don’t where to store parsed information. Any
suggestion?
I presume by BED you mean this format:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1It would be quite useful to be able to parse these kind of files, but
since they are designed for UCSC, it isn’t as simple as ‘implement a
tabbed file parser’. BED data files conventionally generate annotation
tracks, so you would need to implement a datamodel renderer that
generates Jalview style annotation tracks from BED files.As ever, however, the first thing to do is create a new feature on
issues.jalview.org for this, so we can discuss details over there. I’ve
a feeling this might become an EPIC, though, since being able to read
and write BED files could be very useful for people who want to publish
data to UCSC, or import from UCSC.This would also make a great Hackathon topic to work on in Oxford on day
2 of the workshop!Jim.
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
Jim,
I cannot attend to Oxford workshop, though I would like to. I contribute to Jalview only at my free-time (that’s why my contributions are so tiny) and I have no vacations nor budget to go there. Will it be possible to attend by videoconference? May I send you slides for a session about how to develop i18n-compliant code?
Cheers,
D.
2013/11/26 Jim Procter <jprocter@compbio.dundee.ac.uk>
Hi David.
I would like to start my first contact with Jalview development in
deep with a BED parser. I’ve seend BED file format and seems quite
easy to parse so I think I can manage on my own with the parsing but
my problem is that I don’t where to store parsed information. Any
suggestion?
I presume by BED you mean this format:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1It would be quite useful to be able to parse these kind of files, but
since they are designed for UCSC, it isn’t as simple as ‘implement a
tabbed file parser’. BED data files conventionally generate annotation
tracks, so you would need to implement a datamodel renderer that
generates Jalview style annotation tracks from BED files.As ever, however, the first thing to do is create a new feature on
issues.jalview.org for this, so we can discuss details over there. I’ve
a feeling this might become an EPIC, though, since being able to read
and write BED files could be very useful for people who want to publish
data to UCSC, or import from UCSC.This would also make a great Hackathon topic to work on in Oxford on day
2 of the workshop!Jim.
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev_______________________________________________ Jalview-dev mailing list [Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org) [http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)
The University of Dundee is a registered Scottish Charity, No: SC015096
Slides on i18n development would be great, and I’d be happy to dial you in via skype or google hangout.
Jim.
On 26/11/2013 17:40, David Roldán Martínez wrote:
Send me a template (if any), then. My skype is guerrer13. I’ll be available from since 17.30. I hope it won’t be too late. I’ll send you the slides so that you can talk about this, if there is time. 
2013/11/27 Dr JB Procter <jprocter@dundee.ac.uk>
Slides on i18n development would be great, and I’d be happy to dial you in via skype or google hangout.
Jim.
On 26/11/2013 17:40, David Roldán Martínez wrote:
Jim,
I cannot attend to Oxford workshop, though I would like to. I contribute to Jalview only at my free-time (that’s why my contributions are so tiny) and I have no vacations nor budget to go there. Will it be possible to attend by videoconference? May I send you slides for a session about how to develop i18n-compliant code?
Cheers,
D.
_______________________________________________ Jalview-dev mailing list [Jalview-dev@jalview.org](mailto:Jalview-dev@jalview.org) [http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev)The University of Dundee is a registered Scottish Charity, No: SC015096
Jalview-dev mailing list
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2013/11/26 Jim Procter <jprocter@compbio.dundee.ac.uk>
Hi David.
On 25/11/2013 17:03, David Roldán Martínez wrote:
I would like to start my first contact with Jalview development in
deep with a BED parser. I’ve seend BED file format and seems quite
easy to parse so I think I can manage on my own with the parsing but
my problem is that I don’t where to store parsed information. Any
suggestion?
I presume by BED you mean this format:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1It would be quite useful to be able to parse these kind of files, but
since they are designed for UCSC, it isn’t as simple as ‘implement a
tabbed file parser’. BED data files conventionally generate annotation
tracks, so you would need to implement a datamodel renderer that
generates Jalview style annotation tracks from BED files.As ever, however, the first thing to do is create a new feature on
issues.jalview.org for this, so we can discuss details over there. I’ve
a feeling this might become an EPIC, though, since being able to read
and write BED files could be very useful for people who want to publish
data to UCSC, or import from UCSC.This would also make a great Hackathon topic to work on in Oxford on day
2 of the workshop!Jim.
Jalview-dev mailing list
Jalview-dev@jalview.org
http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev