pyani.scripts.subcommands.subcmd_fastani module

class pyani.scripts.subcommands.subcmd_fastani.ComparisonJob

Bases: tuple

Pairwise comparison job for the SQLAlchemy implementation

fastcmd

Alias for field number 2

fragLen

Alias for field number 4

job

Alias for field number 7

kmerSize

Alias for field number 5

minFraction

Alias for field number 6

outfile

Alias for field number 3

query

Alias for field number 0

ref

Alias for field number 1

class pyani.scripts.subcommands.subcmd_fastani.ComparisonResult

Bases: tuple

Convenience struct for a single fastani comparison result.

aln_length

Alias for field number 2

pid

Alias for field number 4

qcov

Alias for field number 7

qid

Alias for field number 0

qlen

Alias for field number 5

rcov

Alias for field number 8

rid

Alias for field number 1

rlen

Alias for field number 6

sim_errs

Alias for field number 3

class pyani.scripts.subcommands.subcmd_fastani.RunData

Bases: tuple

Convenience struct describing an analysis run.

cmdline

Alias for field number 3

date

Alias for field number 2

method

Alias for field number 0

name

Alias for field number 1

pyani.scripts.subcommands.subcmd_fastani.generate_joblist(comparisons: List[T], existingfiles: List[T], args: argparse.Namespace) → List[pyani.scripts.subcommands.subcmd_fastani.ComparisonJob]

Return list of ComparisonJobs

Parameters:

• comparisons – list of (Genome, Genome) tuples for which comparisons are needed
• files (existing) – list of pre-existing FastANI outputs
• args – Namespace, command-line arguments

pyani.scripts.subcommands.subcmd_fastani.run_fastani_jobs(joblist: List[pyani.scripts.subcommands.subcmd_fastani.ComparisonJob], args: argparse.Namespace) → None

Pass fastANI jobs to the scheduler.

Parameters:

• joblist – list of ComparisonJob namedtuples
• args – command-line arguments for the run

pyani.scripts.subcommands.subcmd_fastani.subcmd_fastani(args: argparse.Namespace) → None

Perform fastANI on all genome files in an input directory.

Parameters:args – Namespace, command-line arguments

Finds ANI by the fastANI method, as described in Jain et al (2018) Nature Communications 9, 5114. doi:10.1038/s41467-018-07641-9.

All FASTA format files (selected by suffix) in the input directory are compared against each other, pairwise, using fastANI (whose path must be provided).

For each pairwise comparison, the fastANI .fastani file output is parsed to obtain an alignment length and similarity error countfor the two organisms, as represented by sequences in the FASTA files. These are processed to calculate aligned sequence lengths, average nucleotide identity (ANI) percentages, coverage (aligned percentage of whole genome), and similarity error count for each pairwise comparison.

The calculated values are deposited in the SQLite3 database being used for the analysis.

For each pairwise comparison, the fastANI output is stored in the output directory for long enough to extract summary information, but for each run the output is gzip compressed. Once all runs are complete, the outputs for each comparison are concatenated into a single gzip archive.

pyani.scripts.subcommands.subcmd_fastani.update_comparison_results(joblist: List[pyani.scripts.subcommands.subcmd_fastani.ComparisonJob], run, session, fastani_version: str, args: argparse.Namespace) → None

Update the Comparison table with the completed result set.

Parameters:

• joblist – list of ComparisonJob namedtuples
• run – Run ORM object for the current ANIm run
• session – active pyanidb session via ORM
• fastani_version – version of fastANI used for the comparison
• args – command-line arguments for this run

The Comparison table stores individual comparison results, one per row.