Factoring out tsvreaders

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)
+