Compare commits

..

3 Commits

Author SHA1 Message Date
17932ecd71 Alleles IDs obtained from one sequence is named the ID of that sequence
Some checks failed
autoBIGS.engine/pipeline/head There was a failure building this commit
Instead of generating a tuple comprised of the one sequence ID repeated
2025-02-26 06:15:56 +00:00
6cdc4ff4ae Merge branch 'develop'
Some checks reported errors
autoBIGS.engine/pipeline/tag Something is wrong with the build of this commit
autoBIGS.engine/pipeline/head This commit looks good
2025-02-26 05:26:12 +00:00
62ce1c9b2f Updated README.md to explain versioning
All checks were successful
automlst.engine/pipeline/head This commit looks good
2025-02-18 16:32:02 +00:00
2 changed files with 16 additions and 3 deletions

View File

@ -1,7 +1,8 @@
# autoBIGS.Engine # autoBIGS.engine
A python library implementing common BIGSdb MLST schemes and databases accesses for the purpose of typing sequences automatically. Implementation follows the RESTful API outlined by the official [BIGSdb documentation](https://bigsdb.readthedocs.io/en/latest/rest.html) up to `V1.50.0`. A python library implementing common BIGSdb MLST schemes and databases accesses for the purpose of typing sequences automatically. Implementation follows the RESTful API outlined by the official [BIGSdb documentation](https://bigsdb.readthedocs.io/en/latest/rest.html) up to `V1.50.0`.
## Features ## Features
Briefly, this library can: Briefly, this library can:
@ -22,4 +23,16 @@ Then, it's as easy as running `pip install autobigs-engine` in any terminal that
### CLI usage ### CLI usage
This is a independent python library and thus does not have any form of direct user interface. One way of using it could be to create your own Python script that makes calls to this libraries functions. Alternatively, you may use `autobigs-cli`, a `Python` package that implements a CLI for calling this library. This is a independent python library and thus does not have any form of direct user interface. One way of using it could be to create your own Python script that makes calls to this libraries functions. Alternatively, you may use `autobigs-cli`, a `Python` package that implements a CLI for calling this library.
## Versioning
the autoBIGS project follows [semantic versioning](https://semver.org/) where the three numbers may be interpreted as MAJOR.MINOR.PATCH.
Note regarding major version 0 ([spec item 4](https://semver.org/#spec-item-4)), the following adaptation of semantic versioning definition is as follows:
1. Given x.Y.z, Y is only incremented when a backwards incompatible change is made.
2. Given x.y.Z, Z is only incremented when a backwards compatible change is made.
Versions of autoBIGS items with a major version number of 0 will introduce numerous changes and patches. As such, changes between such versions should be considered highly variable.

View File

@ -127,7 +127,7 @@ class RemoteBIGSdbMLSTProfiler(BIGSdbMLSTProfiler):
raise ValueError("Passed in no alleles.") raise ValueError("Passed in no alleles.")
result_mlst_profile = MLSTProfile(allele_set, scheme_fields_returned["ST"], scheme_fields_returned["clonal_complex"]) result_mlst_profile = MLSTProfile(allele_set, scheme_fields_returned["ST"], scheme_fields_returned["clonal_complex"])
if len(names_list) > 0: if len(names_list) > 0:
result_mlst_profile = NamedMLSTProfile(str(tuple(names_list)), result_mlst_profile) result_mlst_profile = NamedMLSTProfile(str(tuple(names_list)) if len(set(names_list)) > 1 else names_list[0], result_mlst_profile)
return result_mlst_profile return result_mlst_profile
async def profile_string(self, query_sequence_strings: Iterable[Union[NamedString, str]]) -> Union[NamedMLSTProfile, MLSTProfile]: async def profile_string(self, query_sequence_strings: Iterable[Union[NamedString, str]]) -> Union[NamedMLSTProfile, MLSTProfile]: