average_nucleotide_identity.py - average nucleotide identity

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

average_nucleotide_identity.py 0.2.11               July 2021                  AVERAGE_NUCLEOTIDE_IDENTITY.PY(1)

       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]

   optionalarguments:-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).

       average_nucleotide_identity.py - average nucleotide identity