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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py19
1 files changed, 13 insertions, 6 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
index 0604762e..3e216475 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
@@ -24,9 +24,9 @@ import numpy as np
import input
usage = """
-python convertlmm.py [--kinship kfile]
+python convertlmm.py [--plink] [--prefix basename] [--kinship kfile] [--pheno] [--geno]
- Convert files for runlmm.py processing. Writes to stdout.
+ Convert files for runlmm.py processing. Writes to stdout by default.
try --help for more information
"""
@@ -38,8 +38,12 @@ python convertlmm.py [--kinship kfile]
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("--plink", dest="plink",
- help="Parse a phenotype file (PLINK style)")
+option_parser.add_option("--pheno", dest="pheno",
+ help="Parse a phenotype file (use with --plink only)")
+option_parser.add_option("--geno", dest="geno",
+ help="Parse a genotype file (use with --plink only)")
+option_parser.add_option("--plink", dest="plink", default=False,
+ help="Parse PLINK style")
# 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",
@@ -92,7 +96,9 @@ if options.kinship:
wr("\n")
msg(str(count)+" lines written")
-if options.plink:
+if options.pheno:
+ if not options.plink:
+ raise Exception("Use --plink switch")
# Because plink does not track size we need to read the whole thing first
msg("Converting "+options.plink)
phenos = []
@@ -121,5 +127,6 @@ if options.plink:
wr("\t".join(phenos[i]))
wr("\n")
msg(str(count)+" lines written")
-
+
+
msg("Converting done")