diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 19 |
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") |