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) "
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