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authorPjotr Prins2015-03-09 17:14:19 +0300
committerPjotr Prins2015-03-09 17:14:19 +0300
commitf7668a8b9fe552b9d908e2c68367e660d3a81482 (patch)
tree29ccd77dcf049f7b9c955102cdb868e796df66e9
parent749cf072da1849d926ab4d74e288ddf582e84c5a (diff)
downloadgenenetwork2-f7668a8b9fe552b9d908e2c68367e660d3a81482.tar.gz
Add HAB encoding
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py24
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py20
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