diff options
Diffstat (limited to 'wqflask/wqflask/my_pylmm/pyLMM/runlmm.py')
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 20 |
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 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 |