bio_hansel v1.3.2

Fixes:

• #35 ValueError: No objects to concatenate when no tile results are produced

bio_hansel v1.3.1

Adds:

• Version 0.8.0 of Salmonella Enteritidis Scheme.

Fixes:

• Citation fix within the read-me.
• Logo image hosting.

Developer:

• Tests updated for new Enteritidis scheme.

bio_hansel v1.3.0

Fixed:

• Fixed disappearing column; Specify only avg_tile_coverage to be dropped if null.
• Fixed exp vs obs calculation for missing tiles QC check.

Added:

• Added missing tiles QC check on all inconsistent subtypes found in a result
• Added unit test for getting mixed tile counts method

bio_hansel v1.2.0

Fixes:

• incorrect order of parameters for BLAST against FASTA files.

Adds:

• fastqsanger to FASTQ regex
• coverage column for fastq input (avg_tile_coverage column)
• --json command-line option to output JSON representations of output files
• low coverage warning and test
• low coverage parameter

Developer:

• Using kwargs for table and json output.
• Beautifying IF Statements

bio_hansel v1.1.3

README.rst fix

bio_hansel v1.1.2

Fixes #27; QC check for unconfident results where downstream subtype tiles/kmers are missing so it's impossible to call subtype result unambiguously

bio_hansel v1.1.1

Fixes:

• #25 Error in QC join function

bio_hansel v1.1.0

Adds:

• pyahocorasick package for faster subtyping of reads and contigs using a Aho-Corasick Automaton
• Gzipped FASTA/FASTQ support

Fixes:

• #18; default to max-kmer=1000, min-kmer=8
• #21: QC functions no longer expect results from reads

Changes:

• command-line option for --slow run mode for blastn subtyping of contigs and Jellyfish k-mer count subtyping of reads
• Check external dependencies for --slow mode

bio_hansel v1.0.0

Added:

• #14: QC methods for checking for mixed subtypes, intermediate subtypes, too many missing targets, ambiguous subtype result
• #13: technician friendly format (-S) with sample name, subtype result, QC status and QC messages
• SubtypingParams to hold QC and subtyping parameters like min k-mer threshold for subtype calling from reads and max missing tiles for QC
• added qc_status and qc_messages fields to regular summary output
• tests for QC

Fixed:

• check if output files exist, don't overwrite unless --force commandline option set

Changes:

• schemes can have scheme specific subtyping parameters (can add SubtypingParams object to scheme definition)
• updated tests

bio_hansel v0.2.0

Added:

• testing for fastq files, changing input of fasta file to match README documentation
• Travis CI testing; empty __init__.py file that is required to run pytest for CI

Updated:

• #11: schema for Enteritidis to 0.7.0.
• tests
• readme; install instructions

Fixes:

• #4: added version to SCHEME_FASTAS in utils.py and added to Subtype and pd.DataFrame
• #3: check sys.argv length on main.py commandline execution and print help on no args
• #6: Changing all *_total fields to *_expected
• #7: Filtering out unwanted columns in FASTA output
• #10: > to >= in find_inconsistent_subtypes in utils.py; Added tests for enteritidis subtyping scheme