sistr_cmd v1.1.3

Significant updates to the O24-25 antigen containing serovars reporting in line with the current practices. Users can now check the overall SISTR serovar prediction against the list of selected serovars that could be handy for reporting laboratories.

New features:

• The O24 and 25 antigens will not be reported in the antigenic formula.
• Soahanina, Martonos, Midway, Lindern, Bahrenfeld, Moussoro, Amberg, Madelia, Chichiri and Stafford serovars will not be reported and are replaced by other serovars listed in CHANGELOG.md Table 1
• User can now use --list-of-serovars argument to provide a custom list of serovars to check against
• Paratyphi B, Paratyphi B var. Java andI 1,4,[5],12:i:- will get information message in the qc_messages about the d-tartrate testing

For more details on new features and changes please check detailed CHANGELOG.md

New Contributors

• @jameslz made their first contribution in #48

What's Changed

• move EmptyDataError to pandas.errors by @jameslz in #48
• Updated location of SISTR database URL by @apetkau in #51

Full Changelog: v1.1.2...v1.1.3

sistr_cmd v1.1.2

Restricted software dependencies due to them dropping used functionality.

sistr_cmd v1.1.1

• Fixed issue with sorting of BLAST results (causing cgMLST types to be different between BLAST versions). Pull request #43.

sistr_cmd v1.1.0

• Significant updates to SISTR antigen biomarker and cgMLST database

sistr_cmd v1.0.2

Changes:

• tables (PyTables) dependency from 3.4.2 to 3.3.0 for Conda

sistr_cmd v1.0.1

Adds:

• More genomes; 11k to 52790 (thanks Enterobase!)
• Python tables (PyTables) dependency for HDF5 format reading
• cgMLST profiles HDF5 file for faster reading and smaller file size than CSV

Updates:

• cgMLST profiles and alleles databases
• genome to serovar/subspecies tables
• replaced two options for more verbose results with single option (--more-output/-M)
• cleaned up and added new antigen alleles

Fixes:

• Issue #19
• cgMLST result parsing error (allele variable undefined)

sistr_cmd v0.3.6

Removed:

• better_exceptions module since it's not available on Conda

sistr_cmd v0.3.5

Added:

• Default stdout of json.dumps of prediction results when no output dest (-o) specified
• Optional expanded primary prediction output with more detailed results including full blastn results for antigen gene search with bool cmdline args --full-output and --report-blast-results
• Utility output functions for serializing arbitrarily nested objects to dicts with regular literal/scalar values (str, int, float, bool, None) so json.dump(s) doesn't produce an error
• More tests
• better_exceptions (>=0.1.5) module for clearer exception messages (https://github.com/qix-/better-exceptions)

Fixed:

• #18, increments tmp dir name + "_{count}" until new dir success fully created
• No more annoying Pandas warning messages in stderr

sistr_cmd v0.3.4

Changes:

• metavar for -i opt to specify order of args
• replace non-word/whitespace characters in filenames with underscores so that makeblastdb doesn't produce an error
• using genome names instead of file paths for cgMLST results and profiles outputs
• verbose opt default 0 or error only

Fixes:

• check for no input files
• verbose level index out of range error

sistr_cmd v0.3.3

Fixes:

• add back --version cmdline opt