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#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. _______________________________________________ Jalview-dev mailing list [email protected] http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-dev
