ANI_calculator.py [-h] [-d DOWNLOADTOKEN] [-o OUTDIRNAME] [-i INDIRNAME] [-m METHOD]
This program performs a given ANI method (ANIb or ANIm) on a set of input files or downloads a group of files by syncronizing to ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/ and by searching for the DOWNLOADTOKEN
ANIb method: Richter et al (2009) Proc Natl Acad Sci USA 106: 19126-19131 doi:10.1073/pnas.0906412106
ANIm method: Goris et al. (2007) Int J Syst Evol Micr 57: 81-91. doi:10.1099/ijs.0.64483-0
Optional arguments:
-h show this help message and exit
-d DOWNLOADTOKEN Token to search at ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/
-o OUTDIRNAME Output directory
-i INDIRNAME INDIRNAME Input directory name
-m METHOD Method to use (ANIm or ANIb)
ANIm analysis after downloading from NCBI files with Haemophilus_influenzae token: python ANI_calculator.py -d Haemophilus_influenzae -o output -t ANIm
ANIb analysis using files from InpuFiles folder: python ANI_calculator.py -i InputFiles -o output -t ANIb
#Dependencies
For ANI analysis
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Biopython http://www.biopython.org
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NumPy http://www.numpy.org/
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pandas http://pandas.pydata.org/
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SciPy http://www.scipy.org/
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BLAST+ executable in the $PATH, or available on the command line (required for ANIb analysis) ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
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MUMmer executables in the $PATH, or available on the command line (required for ANIm analysis) http://mummer.sourceforge.net/
#Modules used