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ThesisAnnoAlign.
Week 0 (21.10.2009 - 25.10.2009)
- First meeting with David and Marcel
- Recieved topic and short introduction into the topic
- Recieved first supplemental material (3 Papers)
Week 1 (26.10.2009 - 01.11.2009)
- Started working through the material to familiarize myself with the topic
Week 2 (01.11.2009 - 08.11.2009)
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
- prepared a LaTeX structure for the thesis paper