First experimental testing code on FragmentStore usage
Week 3 (08.11.2009 - 15.11.2009)
Wrote summary for the wiki
Started theoretical work on the pipeline
Week 3 & 4 (15.11.2009 - 30.11.2009)
Downloaded and processed testing data (files are not checked into the svn due to file size restrictions and common sense)
Got a Perl script from Marcel that transforms gtf into gff and deletes unneeded records
Wrote code that reads the data into the fragment store and connects each annotation with the corresponding contig (depending on the begin- and endposition)
Open Questions: How to load the read data dynamically as needed?
Perspective: Write a datastructure that aggregates all annotations & the sequence belonging to one "gene" and build a function that creates the splicing products using this datastructure
Week 5 (01.12.2009 - 07.12.2009)
Was really sick, had to stay one day in hospital, therefore couldn't continue work
Weeks 6 - 11 (07.12-2009 - 10.01.2010)
wrote more code to read the data into the according stores (Annotations, AnnotationNames, Contigs)
implemented a new datastructure to gather all annotations belonging to one parent (= a transcript)
investigated an alleged bug in the GTF parser with marcel
Christmas & New Years Eve
Week 12 (11.01.2010 - 18.01.2010)
Meeting with David to work on the above mentioned bug (which was not really a bug rather than a misinterpreted behavior) and to discuss the next steps in the project
Week 13 (18.01.2010 - 25.01.2010)
implemented several sorting steps to ensure that transcript objects are in order in preparation for the splicing proxy construction