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