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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py12
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/plink.py19
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)