average_nucleotide_identity.py

NAME

average_nucleotide_identity.py - average nucleotide identity

DESCRIPTION

usage: average_nucleotide_identity.py [-h] [--version] -o OUTDIRNAME -i

INDIRNAME [-v] [-f] [-s FRAGSIZE]

[-l LOGFILE] [--skip_nucmer] [--skip_blastn] [--noclobber] [--nocompress] [-g] [--gformat GFORMAT] [--gmethod {mpl,seaborn}] [--labels LABELS] [--classes CLASSES] [-m {ANIm,ANIb,ANIblastall,TETRA}] [--scheduler {multiprocessing,SGE}] [--workers WORKERS] [--SGEgroupsize SGEGROUPSIZE] [--SGEargs SGEARGS] [--maxmatch] [--nucmer_exe NUCMER_EXE] [--filter_exe FILTER_EXE] [--blastn_exe BLASTN_EXE] [--makeblastdb_exe MAKEBLASTDB_EXE] [--blastall_exe BLASTALL_EXE] [--formatdb_exe FORMATDB_EXE] [--write_excel] [--rerender] [--subsample SUBSAMPLE] [--seed SEED] [--jobprefix JOBPREFIX]

optional arguments:

-h, --help

show this help message and exit

--version

show program's version number and exit

-o OUTDIRNAME, --outdir OUTDIRNAME

Output directory (required)

-i INDIRNAME, --indir INDIRNAME

Input directory name (required)

-v, --verbose

Give verbose output

-f, --force

Force file overwriting

-s FRAGSIZE, --fragsize FRAGSIZE

Sequence fragment size for ANIb (default 1020)

-l LOGFILE, --logfile LOGFILE

Logfile location

--skip_nucmer

Skip NUCmer runs, for testing (e.g. if output already present)

--skip_blastn

Skip BLASTN runs, for testing (e.g. if output already present)

--noclobber

Don't nuke existing files

--nocompress

Don't compress/delete the comparison output

-g, --graphics

Generate heatmap of ANI

--gformat GFORMAT

Graphics output format(s) [pdf|png|jpg|svg] (default pdf,png,eps meaning three file formats)

--gmethod {mpl,seaborn}

Graphics output method (default mpl)

--labels LABELS

Path to file containing sequence labels

--classes CLASSES

Path to file containing sequence classes

-m {ANIm,ANIb,ANIblastall,TETRA}, --method {ANIm,ANIb,ANIblastall,TETRA}

ANI method (default ANIm)

--scheduler {multiprocessing,SGE}

Job scheduler (default multiprocessing, i.e. locally)

--workers WORKERS

Number of worker processes for multiprocessing (default zero, meaning use all available cores)

--SGEgroupsize SGEGROUPSIZE

Number of jobs to place in an SGE array group (default 10000)

--SGEargs SGEARGS

Additional arguments for qsub

--maxmatch

Override MUMmer to allow all NUCmer matches

--nucmer_exe NUCMER_EXE

Path to NUCmer executable

--filter_exe FILTER_EXE

Path to delta-filter executable

--blastn_exe BLASTN_EXE

Path to BLASTN+ executable

--makeblastdb_exe MAKEBLASTDB_EXE

Path to BLAST+ makeblastdb executable

--blastall_exe BLASTALL_EXE

Path to BLASTALL executable

--formatdb_exe FORMATDB_EXE

Path to BLAST formatdb executable

--write_excel

Write Excel format output tables

--rerender

Rerender graphics output without recalculation

--subsample SUBSAMPLE

Subsample a percentage [0-1] or specific number (1-n) of input sequences

--seed SEED

Set random seed for reproducible subsampling.

--jobprefix JOBPREFIX

Prefix for SGE jobs (default ANI).

AUTHOR

This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.