From 15b3b5b103fdee72a8dc0dac1c9c29e5680fbef9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 7 Mar 2015 11:02:00 +0300
Subject: Kinship converter
---
wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 35 +++++++++++++++++-----------
1 file changed, 21 insertions(+), 14 deletions(-)
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
index 012e96b2..2af84477 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
@@ -24,33 +24,38 @@ import numpy as np
import input
usage = """
-python convertlmm.py [--kinship] infile
+python convertlmm.py [--kinship kfile]
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",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",
+# if len(args) == 0:
+# print usage
+# sys.exit(1)
+
+option_parser = OptionParser(usage=usage)
+option_parser.add_option("--kinship", dest="kinship",
+ help="Parse a kinship file. This is an nxn plain text file and can be computed with the pylmmKinship program")
+# option_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.")
+option_parser.add_option("--prefix", dest="prefix",
+ help="Output prefix for output file(s)")
+option_parser.add_option("-q", "--quiet",
action="store_false", dest="verbose", default=True,
help="don't print status messages to stdout")
+option_parser.add_option("-v", "--verbose",
+ action="store_true", dest="verbose", default=False,
+ help="Print extra info")
-(options, args) = parser.parse_args()
-
-if len(args) == 0:
- print usage
- sys.exit(1)
+(options, args) = option_parser.parse_args()
if options.kinship:
is_header = True
- assert(len(args)==1)
count = 0
- for line in open(args[0],'r'):
+ sys.stderr.write("Converting "+options.kinship+"\n")
+ for line in open(options.kinship,'r'):
count += 1
if is_header:
size = len(line.split())
@@ -64,3 +69,5 @@ if options.kinship:
sys.stdout.write("\t")
sys.stdout.write("\t".join(line.split()))
sys.stdout.write("\n")
+
+sys.stderr.write("Converting done\n")
--
cgit v1.2.3