pyani anib

The anib subcommand will carry out ANIb 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.py anib [-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] [--blastn_exe BLASTN_EXE]
                 [--format_exe FORMAT_EXE] [--fragsize FRAGSIZE]

Flagged arguments

--blastn_exe BLASTN_EXE

Path to the blastn executable. Default: blastn

--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 ANIb process runs. This is useful when testing to avoid aesthetic problems with test output.

--format_exe FORMAT_EXE

Path to the blastn executable. Default: makeblastdb

--fragsize FRAGSIZE

Fragment size to use in analysis. (default: 1020)

-h, --help

Display usage information for pyani anib.

-i INDIR, --input INDIR

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

--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 ANIb process will be written.

--name NAME

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

-o OUTDIR, --outdir OUTDIR

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

--recovery

Use existing ANIb 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)