What is new?

  

v1.3.3 is out ! All the releases can be found here

v1.3.3, February 2025

Minor changes

  • The output file structure has been modified to prepare for the integration of new modules. The output files themselves do not change but their locations on disk do. See this section of the documentation for more details.
  • The documentation now mentions how to install miniforge3 and informs on miniconda3 licencing updates.
  • The following conda dependencies were added to prepare for the integration of new modules: pyarrow, bash, decorator, scipy.
  • The following conda dependencies were upgraded: biopython =1.85, pandas >=2.2, snakemake-minimal >=8, and blast =2.16.

Bug fixes

  • Issue #19 Wrongly reported as duplicate locusTag. Caused by reannot_XerS: the dataframe data was accessed instead of the dataframe df.
  • Issue #20 RuntimeError: Error in IsThereAnIntegraseBetweenThoseTwoConjModule: unrecognized positioning ofICEsIMEsStructureOne. This error happens when 2 relaxases are neighbors on the genome and one of them is found by blastp only while the other one is found by HMM only.
  • Issue #21 RuntimeError: Error in fillUpColocalizedOtherICEsIMEsStructures: ICEsIMEsStructureIT_mostUpstreamStart == -1. In EMStructure.py->listSPsIsContainedWithinOtherStructure, added a parameter to ignore the absence if an SPType was represented in EMStructureToCompareSent.
  • Issue #22 RuntimeError: Error in fillUpColocalizedOtherICEsIMEsStructures: self_mostUpstreamStart == -1. fillUpColocalizedOtherICEsIMEsStructures was not checking for the case when 2 SP of the same type are part of a tuplet.
  • Issue #23 ValueError: End location must be greater than or equal to start location. Cause : method reannot_XerS: df[“CDS_num”] == i was used instead of df[“CDS_num”] == CDS_numTarget.
  • Issue #24 splitListOrderedSPs colocalizeByMaxNumberCDS distanceWithNextSp. Cause : error while reverting a integrase false positive to metadata of the second best blast hit.
  • Issue #25 TypeError: ‘<’ not supported between instances of ‘SP’ and ‘SP’. Cause: def lt(self, other) was not implemented for the object class.
  • Issue #26 ValueError End location. Cause : mishandling of CDS features end location for SP that are re-annotated.
  • Issue #27 Adding Relaxase family domain of most similar ref SP Type Tyrosine integrase.
  • Issue #28 Another case of splitListOrderedSPs colocalizeByMaxNumberCDS. Cause: wrong command line in Error in rule detect_mobile_elements.
  • Issue #29 SP to SeqFeature error. Cause : Biopython error due to misformating of SP matrice in the blastp step.

Updated on 11 Feb 2025