diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py | 21 |
2 files changed, 18 insertions, 12 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index f5ecddb9..bed2e39e 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -57,10 +57,13 @@ cmd = args[0] print "Command: ",cmd if options.kinship: - k = tsvreader.kinship() + k = tsvreader.kinship(options.kinship) + print len(k) if options.pheno: - y = tsvreader.pheno() + y = tsvreader.pheno(options.pheno) + print len(y) if options.geno: - g = tsvreader.geno() + g = tsvreader.geno(options.geno) + print len(g) diff --git a/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py b/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py index 7cea976e..b4027fa3 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py @@ -20,10 +20,10 @@ import os import numpy as np import csv -def kinship(): +def kinship(fn): K1 = [] - print options.kinship - with open(options.kinship,'r') as tsvin: + print fn + with open(fn,'r') as tsvin: assert(tsvin.readline().strip() == "# Kinship format version 1.0") tsvin.readline() tsvin.readline() @@ -32,11 +32,12 @@ def kinship(): ns = np.genfromtxt(row[1:]) K1.append(ns) # <--- slow K = np.array(K1) + return K -def pheno(): +def pheno(fn): Y1 = [] - print options.pheno - with open(options.pheno,'r') as tsvin: + print fn + with open(fn,'r') as tsvin: assert(tsvin.readline().strip() == "# Phenotype format version 1.0") tsvin.readline() tsvin.readline() @@ -46,14 +47,15 @@ def pheno(): ns = np.genfromtxt(row[1:]) Y1.append(ns) # <--- slow Y = np.array(Y1) + return Y -def geno(): +def geno(fn): G1 = [] hab_mapper = {'A':0,'H':1,'B':2,'-':3} pylmm_mapper = [ 0.0, 0.5, 1.0, float('nan') ] - print options.geno - with open(options.geno,'r') as tsvin: + print fn + with open(fn,'r') as tsvin: assert(tsvin.readline().strip() == "# Genotype format version 1.0") tsvin.readline() tsvin.readline() @@ -70,4 +72,5 @@ def geno(): # ns = np.genfromtxt(row[1:]) G1.append(gs2) # <--- slow G = np.array(G1) + return G |