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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/runlmm.py58
-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/tsvreader.py73
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)
+