diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 58 |
1 files changed, 31 insertions, 27 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py index 89c09b1e..3b6b5d70 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py @@ -61,6 +61,8 @@ option_parser.add_option("-v", "--verbose", writer = None num_inds = None +snp_names = [] +ind_names = [] def msg(s): sys.stderr.write("INFO: ") @@ -77,29 +79,6 @@ def wrln(s): wr(s) wr("\n") -if options.kinship: - is_header = True - count = 0 - msg("Converting kinship "+options.kinship) - writer = None - if options.prefix: - writer = open(options.prefix+".kin","w") - for line in open(options.kinship,'r'): - count += 1 - if is_header: - size = len(line.split()) - wrln("# Kinship format version 1.0") - wrln("# Size="+str(size)) - for i in range(size): - wr("\t"+str(i+1)) - wr("\n") - is_header = False - wr(str(count)) - wr("\t") - wr("\t".join(line.split())) - wr("\n") - num_inds = count - msg(str(count)+" kinship lines written") if options.pheno: if not options.plink: @@ -135,19 +114,44 @@ if options.pheno: num_inds = count msg(str(count)+" pheno lines written") +if options.kinship: + is_header = True + count = 0 + msg("Converting kinship "+options.kinship) + writer = None + if options.prefix: + writer = open(options.prefix+".kin","w") + for line in open(options.kinship,'r'): + count += 1 + if is_header: + size = len(line.split()) + wrln("# Kinship format version 1.0") + wrln("# Size="+str(size)) + for i in range(size): + wr("\t"+str(i+1)) + wr("\n") + is_header = False + wr(str(count)) + wr("\t") + wr("\t".join(line.split())) + wr("\n") + num_inds = count + msg(str(count)+" kinship lines written") + if options.geno: msg("Converting geno "+options.geno+'.bed') if not options.plink: raise Exception("Use --plink switch") if not num_inds: raise Exception("Can not figure out the number of individuals, use --pheno or --kinship") - num_snps = plink.readbim(options.geno+'.bim') + bim_snps = plink.readbim(options.geno+'.bim') + num_snps = len(bim_snps) writer = None if options.prefix: writer = open(options.prefix+".geno","w") wrln("# Genotype format version 1.0") wrln("# Individuals = "+str(num_inds)) - wrln("# SNPs = "+str(len(num_snps))) + wrln("# SNPs = "+str(num_snps)) wrln("# Encoding = HAB") for i in range(num_inds): wr("\t"+str(i+1)) @@ -163,8 +167,8 @@ if options.geno: 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 g in range(num_snps): + wr(bim_snps[g][1]+"\t") for i in range(num_inds): wr(m[g][i]) wr("\n") |