pyani.scripts.subcommands.subcmd_anim module

Provides the anim subcommand for pyani.

class pyani.scripts.subcommands.subcmd_anim.ComparisonJob

Bases: tuple

Pairwise comparison job for the SQLAlchemy implementation.

filtercmd

Alias for field number 2

job

Alias for field number 5

nucmercmd

Alias for field number 3

outfile

Alias for field number 4

query

Alias for field number 0

subject

Alias for field number 1

class pyani.scripts.subcommands.subcmd_anim.ComparisonResult

Bases: tuple

Convenience struct for a single nucmer 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

scov

Alias for field number 8

sid

Alias for field number 1

sim_errs

Alias for field number 3

slen

Alias for field number 6

class pyani.scripts.subcommands.subcmd_anim.ProgData

Bases: tuple

Convenience struct for comparison program data/info.

program

Alias for field number 0

version

Alias for field number 1

class pyani.scripts.subcommands.subcmd_anim.ProgParams

Bases: tuple

Convenience struct for comparison parameters.

Use default of zero for fragsize or else db queries will not work as SQLite/Python nulls do not match up well

fragsize

Alias for field number 0

maxmatch

Alias for field number 1

class pyani.scripts.subcommands.subcmd_anim.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_anim.generate_joblist(comparisons: List[Tuple], existingfiles: List[pathlib.Path], args: argparse.Namespace) → List[pyani.scripts.subcommands.subcmd_anim.ComparisonJob]

Return list of ComparisonJobs.

Parameters:

• comparisons – list of (Genome, Genome) tuples
• existingfiles – list of pre-existing nucmer output files
• args – Namespace of command-line arguments for the run

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

Pass ANIm nucmer jobs to the scheduler.

Parameters:

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

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

Perform ANIm on all genome files in an input directory.

Parameters:args – Namespace, command-line arguments

Finds ANI by the ANIm method, as described in Richter et al (2009) Proc Natl Acad Sci USA 106: 19126-19131 doi:10.1073/pnas.0906412106.

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

For each pairwise comparison, the NUCmer .delta file output is parsed to obtain an alignment length and similarity error count for every unique region alignment between the two organisms, as represented by sequences in the FASTA files. These are processed to calculated aligned sequence lengths, average nucleotide identity (ANI) percentages, coverage (aligned percentage of whole genome - forward direction), 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 NUCmer 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_anim.update_comparison_results(joblist: List[pyani.scripts.subcommands.subcmd_anim.ComparisonJob], run, session, nucmer_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
• nucmer_version – version of nucmer used for the comparison
• args – command-line arguments for this run

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