Releases: nmdp-bioinformatics/py-ard
Support reduction of serologically typed GL String
Uses WMDA rel_dna_ser.txt
for the corresponding version of IMGT database to produce serology mapping
Use sqlite3 database for reference data
Use sqlite3 database for data
Offload MAC codes from memory to sqlite3 database (natively supported by Python) to reduce
memory footprint. All MAC lookups happen through the db. The alleles and G group expansions
are still held in memory.
In addition, all generated data is saved as tables in the same database. This leads to one
file for storing all reference data in a standard format.
This led to drastic reduction in memory usage and startup time.
Version | First Time | Prebuilt Data |
---|---|---|
0.1.0 | 10.5 sec | 4.92 sec |
0.2.0 | 814 msec | 598 msec |
0.3.0 | 24.1 msec | 24.7 msec |
Heap memory used by ARD reference data after ard = pyard.ARD(3290)
Version | Memory (MB) |
---|---|
0.1.0 | 2977.86 MB |
0.2.0 | 420.76 MB |
0.3.0 | 3.74 MB |
rearrange data in memory
This release rearranges how memory is used especially MAC codes and a lot of cleanup.
load_mac_file flag to load MAC file
Rename download_mac flag
- Rename
download_mac
ARD flag toload_mac_file
as it properly describes what it does. - Remove dead code
- Reformat code and fix some comments
- Version bumped to
0.1.0
- Updated
pandas
to1.1.2
fix tests and sorting
fixes test and also a bug in 4th field sorting
allow P and G as input, fix lg and lgx behavior
This release fixes the behavior of lg and lgx to always reduce to 2-field.
It also allows P and G alleles as input
Fixes G-codes expansion
Fixes G-codes expansion when smart sorting.
Specify path for temporary files
You can specify path when creating ARD object.
ard = ARD('3290', data_dir='/tmp/py-ard')
version 0.0.16
update MAC location and version to 0.0.16
update to MAC location
0.0.15.0 update version (#37)