Mob-suite

Fixed numpy dependency due to breaking changes in later versions

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 contig_id 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

* 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()`

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

* 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`

• 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