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Alistair Rust authored
The main focus of the debugging has been to implement the get_all_Genes method. For genes with transcripts containing non-sticky exons then things work fine: - get gene - get all transcripts - get all exons - transform exons from raw to assembly coordinates - re-jiggle the exons to which the translation points - re-jiggle the exons to which the transcript points - check that everything translates nicely Sticky exon'ed transcripts are however not playing nicely. This may be a feature of the test database - one of the contigs on which the sticky exon lies may be wrong. The translations of the current test sticky exon is just plain wrong. Retrieving subseqs on the exons are wrong to begin with - pointing therefore at the contig seq. Needs debugging / checking in here. The re-jiggling of translation start/end points for sticky exons needs checking too. The other major related changes are in the seq methods. These now return dna as txt rather than a primary seq object. This makes calls such as seq->seq redundant now. This change has yet to be checked across all modules for consistency yet.
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