Closed alexomics closed 1 year ago
minimap2 already has a python interface, mappy we should aim to re-implement that API so that - in the first instance - this can function as a drop-in replacement.
For this we need:
Aligner
fn_idx_in
fn_idx_out
Aligner.map
Aligner.seq_names
Aligner.seq
None
Alignment
Maybes:
fastx_read(fn, read_comment=False)
revcomp(seq)
minimap2 already has a python interface, mappy we should aim to re-implement that API so that - in the first instance - this can function as a drop-in replacement.
For this we need:
Aligner
argsfn_idx_in
as (MMI)fn_idx_in
as (FA)fn_idx_out
(FA -> MMI)Aligner.map
argsAligner.seq_names
to workAligner.seq
to have the same behaviourNone
on error rather than raiseAlignment
structure with attributesMaybes:
fastx_read(fn, read_comment=False)
revcomp(seq)