pyani anim

The anim subcommand will carry out ANIm analysis using genome files contained in the INDIR directory, writing result files to the OUTDIR directory, and recording data about each comparison and run in a local SQLite3 database.

usage: pyani anim [-h] [-l LOGFILE] [-v] [--debug] [--disable_tqdm] [--version]
                 [--citation] [--scheduler {multiprocessing,SGE}]
                 [--workers WORKERS] [--SGEgroupsize SGEGROUPSIZE]
                 [--SGEargs SGEARGS] [--jobprefix JOBPREFIX] [--name NAME]
                 [--classes CLASSES] [--labels LABELS] [--recovery] -i INDIR
                 -o OUTDIR [--dbpath DBPATH] [--nucmer_exe NUCMER_EXE]
                 [--filter_exe FILTER_EXE] [--maxmatch] [--nofilter]

Flagged arguments

--classes CLASSFNAME

Use the set of classes (one per genome sequence file) found in the file CLASSFNAME in INDIR. Default: classes.txt

--dbpath DBPATH

Path to the location of the local pyani database to be used. Default: .pyani/pyanidb

--disable_tqdm

Disable the tqdm progress bar while the download process runs. This is useful when testing to avoid aesthetic problems with test output.

--filter_exe FILTER_EXE

Path to the MUMmer delta-filter executable. Default: delta-filter

-i INDIR, --indir INDIR

Path to the directory containing indexed genome files to be used for the analysis.

-h, --help

Display usage information for pyani anim.

--jobprefix JOBPREFIX

Use the string JOBPREFIX as a prefix for SGE job submission names. Default: PYANI

--labels LABELFNAME

Use the set of labels (one per genome sequence file) found in the file LABELFNAME in INDIR. Default: labels.txt

-l LOGFILE, --logfile LOGFILE

Provide the location LOGFILE to which a logfile of the download process will be written.

--maxmatch

Use the MUMmer --maxmatch option to include all nucmer matches.

--name NAME

Use the string NAME to identify this ANIm run in the pyani database.

--nofilter

Do not use delta-filter to restrict nucmer output to 1:1 matches.

--nucmer_exe NUCMER_EXE

Path to the MUMmer nucmer executable. Default: nucmer

-o OUTDIR, --outdir OUTDIR

Path to a directory where comparison output files will be written.

--recovery

Use existing NUCmer comparison output if available, e.g. if recovering from a failed job submission. Using this option will not generate a new comparison if the old output files exist.

--scheduler {multiprocessing, SGE}

Specify the job scheduler to be used when parallelising genome comparisons: one of multiprocessing (use many cores on the current machine) or SGE (use an SGE or OGE job scheduler). Default: multiprocessing.

--SGEargs SGEARGS

Pass additional arguments SGEARGS to qsub when running the SGE-distributed jobs.

--SGEgroupsize SGEGROUPSIZE

Create SGE arrays containing SGEGROUPSIZE comparison jobs. Default: 10000

-v, --verbose

Provide verbose output to STDOUT

--workers WORKERS

Spawn WORKERS worker processes with the --scheduler multiprocessing option. Default: 0 (use all cores)