Recent Releases of abstar
abstar - v0.6.0
What's Changed
- Development by @briney in https://github.com/briney/abstar/pull/113
- Add support to write in parquet format by @srgk26 in https://github.com/briney/abstar/pull/115
- Preprocessing by @briney in https://github.com/briney/abstar/pull/116
- Development by @briney in https://github.com/briney/abstar/pull/117
New Contributors
- @srgk26 made their first contribution in https://github.com/briney/abstar/pull/115
Full Changelog: https://github.com/briney/abstar/compare/v0.5.9...v0.6.0
- Pkl
Published by briney about 3 years ago
abstar - v0.4.10
- add the ability for species information to be incorporated into gene names when creating germline databases (helpful for multi-species databases, such as those used for humanized mouse models)
- update makeabstargermline_db to optionally parse species info from gapped IMGT input files and incorporate into the gene names
- replace the vrc01mouse germline database (which contained human IGHV1-2*02 along with all other mouse variable germline genes) with a new humouse database which includes all mouse and human germline genes
- Pkl
Published by briney about 5 years ago
abstar - v0.3.3
Features
- updated macaque germline database with germline sequence information from long-read sequencing of the rhesus macaque genome (by Corey Watson and Shane Crotty, publication pending)
- added a second BaseSpace configuration file (
~/.basespace/default.cfg) which is designed for use with Illumina's BaseMount. As the BaseSpace Python API is not Python 3 compatible,abstarandabcloudwill soon transition to using BaseMount for sequence retrieval rather than the BaseSpace Python API.
Bugfixes
- updated imports in indels.py and mongoimport.py to support Python 3 compatibility
- Pkl
Published by briney about 8 years ago
abstar - 0.2.11
Features
- Added an option (--json-keys) to specify select keys that should be included in the JSON output. Useful if you only want a subset of the default JSON output file. Argument should be a comma-separated list of key names (vgene,dgene,jgene,cdr3aa)
Bugfixes
- Fixed a bug when attempting to use a custom germline database that was named something other than one of the built-in databases
- Pkl
Published by briney over 8 years ago
abstar - 0.1.3
New Features
- Added documentation for ReadTheDocs
abstar.run()now accepts one or sequences as input not just paths to FASTA/Q files- updated the human BLASTn database
- Isotype is now a standalone object, added 'unknown' as an isotype option.
- Added
preprocessmodule
Bug Fixes
- Improved annotation in cases of extreme V/J trimming
- Improved annotation of region-spanning deletions that result in the deletion of an entire FR or CDR
- Improved parsing of junctions with frameshift indels
- Pkl
Published by briney about 10 years ago
abstar - 0.1.2
New features
- Option for compressed output:
-z, --gzip - Option to suppress MongoDB padding from JSON output:
--no-padding
Bugfixes
- Only concatenates appropriate temp files when building final output (previously, would concat all file in temp directory)
- Only deletes appropriate temp files (previously, would empty the entire temp directory)
- Provide a more useful error message when provided with an invalid FASTQ file (if seq and qual lengths don't match, for example)
- Pkl
Published by briney over 10 years ago
abstar -
Fixed a D-gene assignment bug, resulting from improperly created Sequence objects
- Pkl
Published by briney over 10 years ago