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run_create_PDF()
- Calls FPDF class to build PDF report
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format_table_gene_data()
- Formats seperates OXA genes from other gene from main gene dictionary
- Returns two dictionaries of resistance gene information
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format_table_data()
- Formats all data to be printed on PDF
- Return list of table data
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create_phlyo_image()
- Calls mod_tree_text to create a modifiy phylogenetic tree file.
- Takes new newick tree files and creates png file.
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load_matrix()
- Reads in snp matrix data.
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creat_snp_image()
- Creates a png image using snp matrix data.
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mod_tree_text()
- Reads in phylogenetic tree and trims branch data to readability when converted to image.