Convert textual kinship file

1 files changed, 33 insertions, 2 deletions

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
index 4147d90b..35fccef4 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
@@ -17,15 +17,25 @@
 # 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 input
+
 
 usage = """
-Convert files for runlmm.py processing
+python convertlmm.py [--kinship] infile 
+
+  Convert files for runlmm.py processing. Writes to stdout.
+
+  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",
+parser.add_option("--kinship",action="store_false", dest="kinship", default=True,
                   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,
@@ -33,4 +43,25 @@ parser.add_option("-q", "--quiet",
 
 (options, args) = parser.parse_args()
 
+if len(args) == 0:
+    print usage
+    sys.exit(1)
 
+if options.kinship:
+    is_header = True
+    assert(len(args)==1)
+    count = 0
+    for line in open(args[0],'r'):
+        count += 1
+        if is_header:
+            size = len(line.split())
+            print "# Kinship format version 1.0"
+            print "# Size=",size
+            for i in range(size):
+                sys.stdout.write("\t"+str(i+1))
+            sys.stdout.write("\n")
+            is_header = False
+        sys.stdout.write(str(count))
+        sys.stdout.write("\t")
+        sys.stdout.write("\t".join(line.split()))
+        sys.stdout.write("\n")