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-rw-r--r--wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py14
1 files changed, 8 insertions, 6 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
index 3e216475..3932a4d9 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
@@ -24,7 +24,7 @@ import numpy as np
import input
usage = """
-python convertlmm.py [--plink] [--prefix basename] [--kinship kfile] [--pheno] [--geno]
+python convertlmm.py [--plink] [--prefix out_basename] [--kinship kfile] [--pheno pname] [--geno gname]
Convert files for runlmm.py processing. Writes to stdout by default.
@@ -42,7 +42,7 @@ 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,
+option_parser.add_option("--plink", dest="plink", action="store_true", 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.")
@@ -78,6 +78,7 @@ if options.kinship:
is_header = True
count = 0
msg("Converting "+options.kinship)
+ writer = None
if options.prefix:
writer = open(options.prefix+".kin","w")
for line in open(options.kinship,'r'):
@@ -94,17 +95,17 @@ if options.kinship:
wr("\t")
wr("\t".join(line.split()))
wr("\n")
- msg(str(count)+" lines written")
+ msg(str(count)+" kinship lines written")
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)
+ msg("Converting "+options.pheno)
phenos = []
count = 0
count_pheno = None
- for line in open(options.plink,'r'):
+ for line in open(options.pheno,'r'):
count += 1
list = line.split()
pcount = len(list)-2
@@ -115,6 +116,7 @@ if options.pheno:
row = [list[0]]+list[2:]
phenos.append(row)
+ writer = None
if options.prefix:
writer = open(options.prefix+".pheno","w")
wrln("# Phenotype format version 1.0")
@@ -126,7 +128,7 @@ if options.pheno:
for i in range(count):
wr("\t".join(phenos[i]))
wr("\n")
- msg(str(count)+" lines written")
+ msg(str(count)+" pheno lines written")
msg("Converting done")