diff options
| -rw-r--r-- | wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 14 |
1 files changed, 11 insertions, 3 deletions
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py index 3932a4d9..25011b18 100644 --- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py +++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py @@ -21,7 +21,8 @@ import sys import os import numpy as np # from lmm import LMM, run_other -import input +# import input +import plink usage = """ python convertlmm.py [--plink] [--prefix out_basename] [--kinship kfile] [--pheno pname] [--geno gname] @@ -77,7 +78,7 @@ def wrln(s): if options.kinship: is_header = True count = 0 - msg("Converting "+options.kinship) + msg("Converting kinship "+options.kinship) writer = None if options.prefix: writer = open(options.prefix+".kin","w") @@ -101,7 +102,7 @@ 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.pheno) + msg("Converting pheno "+options.pheno) phenos = [] count = 0 count_pheno = None @@ -130,5 +131,12 @@ if options.pheno: wr("\n") msg(str(count)+" pheno lines written") +if options.geno: + if not options.plink: + raise Exception("Use --plink switch") + # msg("Converting geno "+options.geno) + # plink.readbim(options.geno+'.bim') + msg("Converting geno "+options.geno+'.bed') + plink.readbed(options.geno+'.bed',1000,8) msg("Converting done") |