diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 14 |
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") |