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copied!<pre><code>NR>1{ o="1"; z="0"; t="2" if($5 == "T" && $6 == "C") o="T C" if($5 == "T") z="T T" if($6 == "C") t="C C" if($6 == "A") t="A A" for (i=7; i<=NF; i++) { gsub(/1/,o,$i) gsub(/0/,z,$i) gsub(/2/,t,$i) gsub(/-1/,"? ?", $i) } }1 </code></pre> <h3>Output</h3> <pre><code>$ awk -f allele.awk allele.in probeset_id submitted_id chr snp_pos alleleA alleleB 562_201 562_202 562_203 562_204 562_205 562_206 562_207 562_208 562_209 562_210 562_211 562_212 562_213 562_214 562_215 562_216 562_217 562_218 562_219 562_220 562_221 562_222 562_223 562_224 562_225 562_226 562_227 562_228 562_229 562_230 562_231 562_232 562_233 562_234 562_235 562_236 562_237 562_238 562_239 562_240 562_241 562_242 562_243 562_244 562_245 562_246 562_247 562_248 562_249 562_250 562_251 562_252 562_253 562_254 562_255 562_256 562_257 562_258 562_259 562_260 562_261 562_262 562_263 562_264 562_265 562_266 562_267 562_268 562_269 562_270 562_271 562_272 562_273 562_274 562_275 562_276 562_277 562_278 562_279 562_280 562_281 562_283 562_284 562_285 562_289 562_291 562_292 562_294 562_295 562_296 562_400 562_401 562_402 562_403 562_404 562_405 AX-75448119 Chr1_41908741 1 41908741 T C T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T T C T T T T T T T C T C T C T C T C T C T T T C T T T T T T T T C C C C T T T T T T T T T T T C T T T T T T T T T T AX-75448118 Chr1_41908545 1 41908545 T A A A A A A A A A A A A A A A A A A A T T T T T T T T T T T T T T T T T T T T T T 1 A A A A A A A A A A A A A A A A A A T T T T T T T T T T 1 1 T T 1 1 T T T T T T T T T T T T 1 A A A A A A T T 1 1 1 A A ? ? 1 A A T T T T A A 1 1 T T 1 T T 1 A A 1 T T T T 1 A A A A 1 A A A A T T 1 A A A A A A A A A A A A T T 1 T T T T T T 1 A A A A A A A A T T </code></pre> <p><strong>Note</strong>: Your spec is still incomplete, you never say what to do with <code>1</code> when the 5th and 6th columns are not <code>T C</code>, respectively. There are a number of permutations that you are leaving out.</p>

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