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
inINDIR
. 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
inINDIR
. 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 thisANIb
run in thepyani
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) orSGE
(use an SGE or OGE job scheduler). Default:multiprocessing
. --SGEargs SGEARGS
- Pass additional arguments
SGEARGS
toqsub
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)