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MAGI

is a set of scripts for whole genome comparison. It requires python3 and few modules.

Absolute Requirement :

should be compatible with python3

• pandas
• numpy
• biopython

Tips :

for installing all the modules you can use an Anaconda distribution of python3

Other Programs Required to run :

• Emboss
• ProteinOrtho [ tested with v4 ]
• Blastall for running ProteinOrtho
• Prodigal for generating inputs for ProteinOrtho

Instructions:

• Inputs

Input is a directory containing all pep and nuc files

pep and nuc files can be generated using another script called runProdigal.py

File name extension should be Absolutely .pep and .nuc

If you are giving your own .pep and .nuc files be sure that they both have same sequence ids inside Other files in the directory will not be considered

• Output

Output is a csv file containing AGIOS values and number of orthologus pairs between each pair of genomes.

Command Line options :

usage: magi.py [-h] -g GENOME_FILES -p PROTEINORTHO_RESULT_FILE -o OUT_PATH [-c {0,1}]
The main MAGI script.
Inputs are ProteinOrtho result file, path to the cds files , output directory path and calculate agios for core genes
optional arguments:
-h, --help                       show this help message and exit
-g GENOME_FILES                  path to input directory
-p PROTEINORTHO_RESULT_FILE      path to ProteinOrtho result file
-o OUT_PATH                      Out put directory path
-c {0,1}                         calculate agios for core genes (0 for no cores 1 for yes)

Using Accessory Scripts :

Running Prodigal

usage: runProdigal.py [-h] -g GENOME_LIST [GENOME_LIST ...]
This is a suplimentary script which runs prodigal and parse the file and give correct filenames
Requirements: prodigal
optional arguments:
-h, --help                         show this help message and exit
-g GENOME_LIST [GENOME_LIST ...]   path to the genome files

PreProcessing

need to update this script

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To Do

• working on threading for improving speed

Citation

• A polyphasic strategy incorporating genomic data for the taxonomic description of novel bacterial species.International Journal of Systematic and Evolutionary Microbiology (2014), 64 ,384-391. [DOI: 10.1099/ijs.0.057091-0] .