Kinship 1.0 parser

1 files changed, 70 insertions, 0 deletions

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
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+# This is the LMM runner that calls the possible methods using command line
+# switches. It acts as a multiplexer where all the invocation complexity
+# is kept outside the main LMM routines.
+#
+# 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/>.
+
+from optparse import OptionParser
+import sys
+import os
+import numpy as np
+# from lmm import LMM, run_other
+import csv
+
+
+usage = """
+python runlmm.py [options] command
+
+  runlmm.py processing multiplexer reads standard input types and calls the routines
+
+  Current commands are:
+
+    parse        : only parse input files
+
+  try --help for more information
+"""
+
+parser = OptionParser(usage=usage)
+# parser.add_option("-f", "--file", dest="input file",
+#                   help="In", metavar="FILE")
+parser.add_option("--kinship",dest="kinship",
+                  help="Kinship file format")
+parser.add_option("-q", "--quiet",
+                  action="store_false", dest="verbose", default=True,
+                  help="don't print status messages to stdout")
+
+(options, args) = parser.parse_args()
+
+if len(args) != 1:
+    print usage
+    sys.exit(1)
+
+cmd = args[0]
+print "Command: ",cmd
+
+if options.kinship:
+    K1 = []
+    print options.kinship
+    with open(options.kinship,'r') as tsvin:
+        if tsvin.readline().strip() != "# Kinship format version 1.0":
+            raise Exception("Expecting 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)