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

sistr_cmd v0.3.2

Fixes:

• skip writing of null/None novel alleles

Adds:

• option (-i/--input-fasta-genome-name; -i /path/to/g1.fa genome1) to specify genome names along with path to fasta
• tab-delimited results output "-f tab"