Open ssnn-airr opened 6 years ago
Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
Maybe it would be better to make this a MakeDb-airr command, given the decision to switch the core format to the AIRR standard. The basic functionality would be to take in an AIRR Rearrangement file and do a little standardization within that scope. For now, I see this only entailing:
sequence_alignment
and germline_alignment
and modifying the appropriate germline start/end fields.productive
and junction_aa
based on the junction
frame._cigar
fields.locus
field if needed.All as options, because the input AIRR file could come from any source, not just IgBLAST.
Original comment by Scott Christley (Bitbucket: [Scott Christley](https://bitbucket.org/Scott Christley), ).
Is this mainly dealing with different fields names, or does new functionality need to be written? I would also vote for the IMGT gapped alignments to be put in new fields instead of overwriting the existing field content.
Original comment by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
Some new functionality is needed, which is why it’s taking me so long to get around to it. The bottleneck testing the existing IMGT-gapping methods on different outputs. The field renaming stuff and conversion from _length
to _end
is all already in ConvertDb.
Original report by Jason Vander Heiden (Bitbucket: javh, GitHub: javh).
Look into the behavior of the
-r
argument to ConvertDb-airr and ConvertDb-changeo. It doesn't seem correct, at a glance.