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Thank you for the very informative post.

I followed your instructions and the output printed perfectly into the command line. I changed the file extensions around (to BSAC.txt and Script.pl) and obtained the same result - uninitialised value errors and the Number of Strains and AA Change columns were left blank.

I decided to try pasting the rest of my file under the __DATA__ part of your code. For the most part it worked as expected, but with interspersed Use of uninitialised value within %cod in string eq at Script.pl line 32, <DATA> line XXX.. These lines are referring to non-synonymous mutations that code for a STOP codon, like the one below-

FT SNP 2811491 FT /note="refAllele: G SNPstrains: 7414_8#89=A (SNP codon is ST +OP) (AA Gln->STOP) " FT /colour=4
I assume this is because the code has not matched 'non' in the line. Could this also be the cause of my uninitialised value error in the original post?

Many Thanks

In reply to Re^8: Parsing problem by MB123
in thread Parsing problem by MB123

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