MAUVE_SNPs

mauve_to_snps.py locates if a SNP is within the range of annotated features when given a gbk annotation file and the output of the SNP exporter tool in Mauve.

• Takes the reference (or first) gbk input for progressiveMauve alignment and SNP export file as input. (script will use only the first column of the SNP file)

• Outputs a list of SNPS in annotated regions only (eg. will exclude anything outside the range of annotated tRNA, rRNA or CDS positions but will notify when it encouters a SNP in region with no annotation)

    USAGE: mauve_to_snps.py Exported_SNPS.txt  first_gbk_file > snps.txt  
  

Note that this won't be foolproof for mis-annotations!....always check the alignment..

Output looks like:

NODE_1: SNP here but no annotations found!
Node: NODE_3
Product: hypothetical_protein
Value: 17
Range: 13, 210
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Node: NODE_15
Product: Small_toxic_polypeptide_LdrD
Value: 596
Range: 596, 723
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