nref, p, logodds, pval, nother, sum(counts.values()), duplicates_removed, len(reads), total] outrows.append(row) progress.update() progress.done() progress.stage('Multiple-test correction and FDR computation') bonf = bonferroni(pvalues) fdr = fdr(pvalues) i = 0 pvalpos = outheaders.index('P-Value') for r in outrows: if len(r) > pvalpos: if r[pvalpos] != emptysym: r.insert(pvalpos + 1, fdr[i]) r.insert(pvalpos + 1, bonf[i]) i += 1 else: r.insert(pvalpos + 1, emptysym) r.insert(pvalpos + 1, emptysym) progress.done()
for s in sorted(BadRead.allheaders): row.append(badread[s]) outrows.append(row) if not any: # ["%s:%d_%s/%s"%(snpchr,snppos,ref,alt)] \ outrows.append([snpchr, snppos, ref, alt] + [snpextra.get(k, emptysym) for k in extrasnpheaders] + [0]) progress.update() progress.done() progress.stage('Multiple-test correction and FDR computation') bonf = bonferroni(pvalues) fdr = fdr(pvalues) i = 0 pvalpos = outheaders.index('P-Value') for r in outrows: if len(r) > pvalpos: if r[pvalpos] != emptysym: r.insert(pvalpos + 1, fdr[i]) r.insert(pvalpos + 1, bonf[i]) i += 1 else: r.insert(pvalpos + 1, emptysym) r.insert(pvalpos + 1, emptysym) progress.done()