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.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.11.
.TH AVERAGE_NUCLEOTIDE_IDENTITY.PY "1" "November 2019" "average_nucleotide_identity.py 0.2.9" "User Commands"
.SH NAME
average_nucleotide_identity.py \- average nucleotide identity
.SH SYNOPSIS
.B average_nucleotide_identity.py
[\-h] [\-\-version] \fB\-o\fR OUTDIRNAME \fB\-i\fR 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]
.SH OPTIONS
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-o\fR OUTDIRNAME, \fB\-\-outdir\fR OUTDIRNAME
Output directory (required)
.TP
\fB\-i\fR INDIRNAME, \fB\-\-indir\fR INDIRNAME
Input directory name (required)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Give verbose output
.TP
\fB\-f\fR, \fB\-\-force\fR
Force file overwriting
.TP
\fB\-s\fR FRAGSIZE, \fB\-\-fragsize\fR FRAGSIZE
Sequence fragment size for ANIb (default 1020)
.TP
\fB\-l\fR LOGFILE, \fB\-\-logfile\fR LOGFILE
Logfile location
.TP
\fB\-\-skip_nucmer\fR
Skip NUCmer runs, for testing (e.g. if output already
present)
.TP
\fB\-\-skip_blastn\fR
Skip BLASTN runs, for testing (e.g. if output already
present)
.TP
\fB\-\-noclobber\fR
Don't nuke existing files
.TP
\fB\-\-nocompress\fR
Don't compress/delete the comparison output
.TP
\fB\-g\fR, \fB\-\-graphics\fR
Generate heatmap of ANI
.TP
\fB\-\-gformat\fR GFORMAT
Graphics output format(s) [pdf|png|jpg|svg] (default
pdf,png,eps meaning three file formats)
.TP
\fB\-\-gmethod\fR {mpl,seaborn}
Graphics output method (default mpl)
.TP
\fB\-\-labels\fR LABELS
Path to file containing sequence labels
.TP
\fB\-\-classes\fR CLASSES
Path to file containing sequence classes
.TP
\fB\-m\fR {ANIm,ANIb,ANIblastall,TETRA}, \fB\-\-method\fR {ANIm,ANIb,ANIblastall,TETRA}
ANI method (default ANIm)
.TP
\fB\-\-scheduler\fR {multiprocessing,SGE}
Job scheduler (default multiprocessing, i.e. locally)
.TP
\fB\-\-workers\fR WORKERS
Number of worker processes for multiprocessing
(default zero, meaning use all available cores)
.TP
\fB\-\-SGEgroupsize\fR SGEGROUPSIZE
Number of jobs to place in an SGE array group (default
10000)
.TP
\fB\-\-SGEargs\fR SGEARGS
Additional arguments for qsub
.TP
\fB\-\-maxmatch\fR
Override MUMmer to allow all NUCmer matches
.TP
\fB\-\-nucmer_exe\fR NUCMER_EXE
Path to NUCmer executable
.TP
\fB\-\-filter_exe\fR FILTER_EXE
Path to delta\-filter executable
.TP
\fB\-\-blastn_exe\fR BLASTN_EXE
Path to BLASTN+ executable
.TP
\fB\-\-makeblastdb_exe\fR MAKEBLASTDB_EXE
Path to BLAST+ makeblastdb executable
.TP
\fB\-\-blastall_exe\fR BLASTALL_EXE
Path to BLASTALL executable
.TP
\fB\-\-formatdb_exe\fR FORMATDB_EXE
Path to BLAST formatdb executable
.TP
\fB\-\-write_excel\fR
Write Excel format output tables
.TP
\fB\-\-rerender\fR
Rerender graphics output without recalculation
.TP
\fB\-\-subsample\fR SUBSAMPLE
Subsample a percentage [0\-1] or specific number (1\-n)
of input sequences
.TP
\fB\-\-seed\fR SEED
Set random seed for reproducible subsampling.
.TP
\fB\-\-jobprefix\fR JOBPREFIX
Prefix for SGE jobs (default ANI).
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and
can be used for any other usage of the program.
|
