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| author | Pjotr Prins | 2015-03-09 16:47:33 +0300 |
|---|---|---|
| committer | Pjotr Prins | 2015-03-09 16:47:33 +0300 |
| commit | 749cf072da1849d926ab4d74e288ddf582e84c5a (patch) | |
| tree | 2d79b136bb77309178508cce671bc7495217c105 | |
| parent | 02cb9710a83bc81abe198cb089dc5a70baf1b657 (diff) | |
| download | genenetwork2-749cf072da1849d926ab4d74e288ddf582e84c5a.tar.gz | |
Write genotype file non-transposed
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 12 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/plink.py | 19 |
2 files changed, 16 insertions, 15 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py index a3728bd2..f35cc47c 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py @@ -148,17 +148,17 @@ if options.geno: wrln("# Genotype format version 1.0") wrln("# Individuals = "+str(num_inds)) wrln("# Phenotypes = "+str(len(num_snps))) + for i in range(len(num_snps)): + wr("\t"+str(i+1)) + wr("\n") + m = [] def out(i,x): wr(str(i)+"\t") - lst = [str(v) for v in x] - wr("\t".join(lst)) + wr("\t".join(x)) wr("\n") - snps = plink.readbed(options.geno+'.bed',num_inds, out) - # for i in range(num_snps): - # wr("\t"+str(i+1)) - # wr("\n") + snps = plink.readbed(options.geno+'.bed',num_inds, ('A','H','B','NA'), out) # for i in range(count): # wr("\t".join(phenos[i])) # wr("\n") diff --git a/wqflask/wqflask/my_pylmm/pyLMM/plink.py b/wqflask/wqflask/my_pylmm/pyLMM/plink.py index 4ad2c5f7..7bd2df91 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/plink.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/plink.py @@ -66,25 +66,26 @@ def readbim(fn): # http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html#fam # http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html#bim -def readbed(fn,inds,func=None): +def readbed(fn,inds,encoding,func=None): # For every SNP block fetch the individual genotypes using values # 0.0 and 1.0 for homozygous and 0.5 for heterozygous alleles def fetchGenotypes(X): - D = { \ - '00': 0.0, \ - '10': 0.5, \ - '11': 1.0, \ - '01': float('nan') \ - } - + # D = { \ + # '00': 0.0, \ + # '10': 0.5, \ + # '11': 1.0, \ + # '01': float('nan') \ + # } + + Didx = { '00': 0, '10': 1, '11': 2, '01': 3 } G = [] for x in X: if not len(x) == 10: xx = x[2:] x = '0b' + '0'*(8 - len(xx)) + xx a,b,c,d = (x[8:],x[6:8],x[4:6],x[2:4]) - L = [D[y] for y in [a,b,c,d]] + L = [encoding[Didx[y]] for y in [a,b,c,d]] G += L G = G[:inds] # G = np.array(G) |