diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/runlmm.py | 58 | ||||
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py | 73 |
2 files changed, 78 insertions, 53 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py index ce8e32be..f5ecddb9 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py @@ -18,12 +18,7 @@ # along with this program. If not, see <http://www.gnu.org/licenses/>. from optparse import OptionParser -import sys -import os -import numpy as np -# from lmm import LMM, run_other -import csv - +import tsvreader usage = """ python runlmm.py [options] command @@ -38,6 +33,7 @@ python runlmm.py [options] command try --help for more information """ + parser = OptionParser(usage=usage) # parser.add_option("-f", "--file", dest="input file", # help="In", metavar="FILE") @@ -61,54 +57,10 @@ cmd = args[0] print "Command: ",cmd if options.kinship: - K1 = [] - print options.kinship - with open(options.kinship,'r') as tsvin: - assert(tsvin.readline().strip() == "# Kinship format version 1.0") - tsvin.readline() - tsvin.readline() - tsv = csv.reader(tsvin, delimiter='\t') - for row in tsv: - ns = np.genfromtxt(row[1:]) - K1.append(ns) # <--- slow - K = np.array(K1) + k = tsvreader.kinship() 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) + y = tsvreader.pheno() if options.geno: - 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: - 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) - id = row[0] - gs = list(row[1]) - # print id,gs - gs2 = [pylmm_mapper[hab_mapper[g]] for g in gs] - # print id,gs2 - # ns = np.genfromtxt(row[1:]) - G1.append(gs2) # <--- slow - G = np.array(G1) - -print G + g = tsvreader.geno() diff --git a/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py b/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py new file mode 100644 index 00000000..7cea976e --- /dev/null +++ b/wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py @@ -0,0 +1,73 @@ +# Standard file readers +# +# Copyright (C) 2015 Pjotr Prins (pjotr.prins@thebird.nl) +# +# This program is free software: you can redistribute it and/or modify +# it under the terms of the GNU Affero General Public License as +# published by the Free Software Foundation, either version 3 of the +# License, or (at your option) any later version. + +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Affero General Public License for more details. + +# You should have received a copy of the GNU Affero General Public License +# along with this program. If not, see <http://www.gnu.org/licenses/>. + +import sys +import os +import numpy as np +import csv + +def kinship(): + K1 = [] + print options.kinship + with open(options.kinship,'r') as tsvin: + assert(tsvin.readline().strip() == "# Kinship format version 1.0") + tsvin.readline() + tsvin.readline() + tsv = csv.reader(tsvin, delimiter='\t') + for row in tsv: + ns = np.genfromtxt(row[1:]) + K1.append(ns) # <--- slow + K = np.array(K1) + +def 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) + +def geno(): + 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: + 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) + id = row[0] + gs = list(row[1]) + # print id,gs + gs2 = [pylmm_mapper[hab_mapper[g]] for g in gs] + # print id,gs2 + # ns = np.genfromtxt(row[1:]) + G1.append(gs2) # <--- slow + G = np.array(G1) + |