Helpers to split out functionality

2 files changed, 56 insertions, 0 deletions

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
new file mode 100644
index 00000000..4147d90b
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
@@ -0,0 +1,36 @@
+# This is a converter for common LMM formats, so as to keep complexity
+# outside the main 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
+
+usage = """
+Convert files for runlmm.py processing
+"""
+
+parser = OptionParser(usage=usage)
+# parser.add_option("-f", "--file", dest="input file",
+#                   help="In", metavar="FILE")
+parser.add_option("--kinship",
+                  help="Parse a kinship file. This is an nxn plain text file and can be computed with the pylmmKinship program.")
+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()
+
+
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
new file mode 100644
index 00000000..df86f718
--- /dev/null
+++ b/wqflask/wqflask/my_pylmm/pyLMM/runlmm.py
@@ -0,0 +1,20 @@
+# 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/>.
+
+