mob-suite - v3.1.8 - Improved biomarkers report consistency

This release includes small but important convenience fixes such as fix to #152 issue where in cases when there are absolutely no plasmid biomarkers (i.e. empty biomarkers report) mob_typer would fail. Additionally, this release improves marker reporting consistency between biomarkers and the main plasmid typing reports generated by mobrecon and mobtyper. The biomarkers report introduced since v3.1.7 lists the main plasmid biomarkers and their coordinates. Finally, plasmid databases were cleaned, synced and redundant files removed. A new databases archive url was updated and now points to https://zenodo.org/records/10304948/files/data.tar.gz?download=1

• Fixed permanently issue #152 and added a unit test test_mob_recon_no_plasmid_biomarkers()
• Updated the core database archive data.tar.gz: a) removed redundant host_range_ncbirefseq_plasmidDB.txt and host_range_ncbirefseq_plasmidDB.csv; b) updated clusters.txt with new mob_typer biomarker results for consistency (the cluster codes and number of records did not change)
• Improved biomarkers report consistency with other reports by making sure that all markers listed in the mob_typer report are present in the biomarkers report. Implemented a new unit tests listed in test_databases_consistency.py

- Python
Published by kbessonov1984 over 2 years ago

mob-suite - Addition of filtered biomarker blast report

This release includes a fix to #150 where uninitialized databases to mobtyper would result in confusing error messages. Additionally, this release includes the addition of a new biomarkers blast report file which will be automatically generated by mobrecon and optionally by mobtyper if the --biomarkerreport_file parameter is included. This file contains the filtered biomarker blast results for oriT, replicon, relaxase, and mate-pair-formation as a single tab-delimited file of blast results with an included column labelling which biomarker type the sequence belongs to.

- Python
Published by jrober84 almost 3 years ago

mob-suite - MOB-cluster bug fixes

This update includes fixes to issues #149 with thanks to @rpetit3 additionally, addresses the generation of mge reports with empty results when called through mob-typer

- Python
Published by jrober84 almost 3 years ago

mob-suite - MOB-cluster bug fixes

Largely resolving issues with MOB-cluster not running due to changes in ETE3 DB parameters

- Python
Published by jrober84 almost 3 years ago

mob-suite - Indentation fix and version bump

Fixed an issue with ETE3 database not being set with default database

- Python
Published by jrober84 over 3 years ago

mob-suite - MOB-suite v 3.1.2

Fixed numpy dependency due to breaking changes in later versions

- Python
Published by jrober84 over 3 years ago

mob-suite - MOB-suite: Addition of MGE detection and minor bug fixes v3.1.0

MOB-suite v3.1.0 adds in a reporting of mobile genetic elements (MGE) based on the repetitive masking file comprised of IS/TN elements. It will report the blast HSP results combined with the molecule_type and primary MOB-cluster. This MGE report file will be created by default with MOB-recon and is optional with MOB-typer by specifying a report file.

This release also addresses several different issues:

MOB-recon and MOB-typer will now report out the original contigid supplied in fasta files instead of converting spaces to "" #99, #87 #85 MOB-recon has re-implemented the maximum contig size and plasmid size restrictions #101 MOB-recon has removed the -t flag as typer is always invoked #100 MOB-recon and MOB-typer will no longer restrict threads to 1 for tblastn searches #96 #104 Removed ETE3 lock file mechanism #93 Default argument values are now visible when using --help #91

- Python
Published by jrober84 about 4 years ago

mob-suite - Make MOB-Suite read-only file system friendly

• Fixes issue #82 and issue #63
• Fixes file permissions for plasmid database files by not copying original permissions from data.tar.gz
• Fixes mob_init start on systems with python binary defined other than python thanks to use of sys.executable variable in verify_init()

- Python
Published by kbessonov1984 almost 5 years ago

mob-suite - Fixed broken database mirror

This release is purely to address broken download links for the database

- Python
Published by jrober84 almost 5 years ago

mob-suite - Minor update for better compatibility with pandas and ete3 libs

• Addressed issues #70 #61 related to pandas > 1.0.5 and EmptyDataError exception import
• Duplication taxonomy identifiers issue #65 during ete3 library initialization that was solved in version 3.1.2

- Python
Published by kbessonov1984 over 5 years ago

mob-suite - Major revision to MOB-suite

• MOB-clusters have been completely changed to utilize an updated clustering approach and threshold. Clusters are now issued accession numbers instead of numeric codes in the format of [A-Z][A-Z][0-9] [0-9] [0-9] [0-9] to prevent any mixed use of clusters from previous versions. Mappings of samples to previous codes is provided in cluster_mapping.txt • Reference database of plasmids has increased to ~23K closed plasmid sequences for use in reconstruction and comparison • Biomarker databases have had minor changes to incorporate new sequences and updates to nomenclature • Added functionality for users to supply sequences at runtime for MOB-recon to ignore based on their specific datasets • Added functionality for chromosome depletion based on closed reference sequences. This is a more flexible approach than the user defined filter sequences as it will only use close genomes for filtering. • MOB-typer now allows for processing batches of unrelated plasmids in the same file using the –multi flag • Improved performance by re-using MOB-recon biomarker results instead of calling MOB-typer on each reconstructed plasmid • Removed dependency on circulator and incorporated an overhang detection using a process similar to berroka https://github.com/tseemann/berokka • Output files produced by MOB-suite have changed and may break any existing pipelines based on the output files

- Python
Published by jrober84 about 6 years ago

mob-suite - MOB-recon algorithm update

• Removed the requirement for circlator due to issues with installing that package and have implemented a blast based method for detecting circular overhangs of contigs.
• Significantly improved assignment of contigs where a close reference sequence is in the database
• Fixed issue #35
• Fixed issue with MOB-cluster writing the incorrect level of clustering to fasta files

- Python
Published by jrober84 over 6 years ago

mob-suite - Stable host range release

• Fixed issue #36 by making removing all non-ascii characters in the database file and removing any potential printing to the screen avoiding UnicodeEncodeError
• Fixed issue #35 with software version displayed as 2.0.5 without any braces
• Fixed logging level inheritance from the root logger.
• Fixed issue #41 avoiding mean calculation on non int or float values

- Python
Published by kbessonov1984 over 6 years ago

mob-suite - Improved stability on non-standard locales and migrated ete3 taxonomy database to databases folder

• Made mob_suite independent of the system locale and character encoding settings
• moved all ete3 databases to the tool /databases/ folder for easy maintenance and compatibility.
• improved ete3 initialization routines inside mob_hostrage module preventing race condition
• added --version switch to all tools
• addressed issues issue #35, #36, #38 , #39 and #40

- Python
Published by kbessonov1984 over 6 years ago

mob-suite - MOB-Suite 2.0.1 with no graphical dependency on ete3 library

• This version improves on stability of the 2.0.0 version by removing dependency on TreeStyle submodule from the ete3 library which caused some issues on the server machines without mesa graphical libraries (see issue #28)
• Implemented folder lock functionality for the mob_init script preventing race condition on multiple mob_suite initialization instances
• Implemented test function for conda package testing
• Corrected issue #29 allowing mob_init to initialize ete3 library taxonomy
• Included singularity image recipe and updated README.md

- Python
Published by kbessonov1984 over 6 years ago

mob-suite - MOB-host range and transfer rate prediction module. First release

Added plasmid host range and transfer rate predictions. Corrected previous bugs related to a) empty mobaggregatereport.txt when running mob_recon; b) results reporting for multi-replicon plasmids;

- Python
Published by kbessonov1984 almost 7 years ago

mob-suite - New download mirrors added and new parameters to specify reference databases

Previous FigShare mirror changed. We added new mirror at shared.corefacility.ca host allowing for faster downloads and better reliability. Now we have two download mirrors at share.corefacility.ca and ndownloader.figshare.com. As per user requests we've added ability to specify reference databases directory via the --database_directory and other parameters (see command-line help).

- Python
Published by kbessonov1984 over 7 years ago

mob-suite - Bug fixes and documentation update

There was an error where blast databases were being rebuilt on each run which was inefficient and resulted in a race condition when large numbers of parallel jobs were running.

- Python
Published by jrober84 over 7 years ago

mob-suite - Minor bug fixes with numerical parameters

- Python
Published by jrober84 almost 8 years ago

mob-suite - Minor bug fixes

- Python
Published by jrober84 almost 8 years ago

mob-suite - Updated Error handling

- Python
Published by jrober84 almost 8 years ago

mob-suite - Conda initial release

- Python
Published by jrober84 about 8 years ago

mob-suite - Initial Release of the MOB-suite

Initial release of the MOB-suite software ported to python 3 for distribution in Conda

- Python
Published by jrober84 about 8 years ago