diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 24 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 20 |
2 files changed, 34 insertions, 10 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py index f35cc47c..8a1f03ad 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py @@ -148,20 +148,26 @@ 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)): + for i in range(num_inds): wr("\t"+str(i+1)) - wr("\n") + wr("\n") m = [] def out(i,x): - wr(str(i)+"\t") - wr("\t".join(x)) - wr("\n") + # wr(str(i)+"\t") + # wr("\t".join(x)) + # wr("\n") + m.append(x) - 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") + snps = plink.readbed(options.geno+'.bed',num_inds, ('A','H','B','-'), out) + + msg("Write transposed genotype matrix") + for g in range(len(num_snps)): + wr(str(g+1)+"\t") + for i in range(num_inds): + wr(m[g][i]) + wr("\n") + msg(str(count)+" geno lines written (with "+str(snps)+" snps)") msg("Converting done") diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index 27afd6f4..4398926f 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -44,6 +44,8 @@ parser.add_option("--kinship",dest="kinship", help="Kinship file format 1.0") parser.add_option("--pheno",dest="pheno", help="Phenotype file format 1.0") +parser.add_option("--geno",dest="geno", + help="Genotype file format 1.0") parser.add_option("-q", "--quiet", action="store_false", dest="verbose", default=True, help="don't print status messages to stdout") @@ -84,4 +86,20 @@ if options.pheno: Y1.append(ns) # <--- slow Y = np.array(Y1) -print Y +if options.geno: + G1 = [] + print options.geno + with open(options.geno,'r') as tsvin: + assert(tsvin.readline().strip() == "# Genotype format version 1.0") + tsvin.readline() + tsvin.readline() + tsvin.readline() + tsvin.readline() + tsv = csv.reader(tsvin, delimiter='\t') + for row in tsv: + print(row) + # ns = np.genfromtxt(row[1:]) + G1.append(ns) # <--- slow + G = np.array(G1) + +print G |