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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py20
1 files changed, 19 insertions, 1 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
index 4a640d6d..27afd6f4 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -41,7 +41,9 @@ parser = OptionParser(usage=usage)
# parser.add_option("-f", "--file", dest="input file",
# help="In", metavar="FILE")
parser.add_option("--kinship",dest="kinship",
- help="Kinship file format")
+ help="Kinship file format 1.0")
+parser.add_option("--pheno",dest="pheno",
+ help="Phenotype file format 1.0")
parser.add_option("-q", "--quiet",
action="store_false", dest="verbose", default=True,
help="don't print status messages to stdout")
@@ -67,3 +69,19 @@ if options.kinship:
ns = np.genfromtxt(row[1:])
K1.append(ns) # <--- slow
K = np.array(K1)
+
+if options.pheno:
+ Y1 = []
+ print options.pheno
+ with open(options.pheno,'r') as tsvin:
+ assert(tsvin.readline().strip() == "# Phenotype format version 1.0")
+ tsvin.readline()
+ tsvin.readline()
+ tsvin.readline()
+ tsv = csv.reader(tsvin, delimiter='\t')
+ for row in tsv:
+ ns = np.genfromtxt(row[1:])
+ Y1.append(ns) # <--- slow
+ Y = np.array(Y1)
+
+print Y