From d924bc5842d2813aad8359b9cb614c2a87df1ee9 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 9 Mar 2015 14:37:04 +0300
Subject: plink: missing values in bim

---
 wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py | 27 +++++++++++++++++++--------
 wqflask/wqflask/my_pylmm/pyLMM/plink.py      |  2 ++
 2 files changed, 21 insertions(+), 8 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
index 173bae2e..d04f9b94 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/convertlmm.py
@@ -136,19 +136,30 @@ if options.pheno:
     msg(str(count)+" pheno lines written")
 
 if options.geno:
+    msg("Converting geno "+options.geno+'.bed')
     if not options.plink:
         raise Exception("Use --plink switch")
     if not num_inds:
         raise Exception("Can not figure out the number of individuals, use --pheno or --kinship")    
-    # msg("Converting geno "+options.geno)
-
-    snps = plink.readbim(options.geno+'.bim')
-    msg("Converting geno "+options.geno+'.bed')
-
-    # def out(i,x):
-    #     print i,x
+    num_snps = plink.readbim(options.geno+'.bim')
+    writer = None
+    if options.prefix:
+        writer = open(options.prefix+".geno","w")
+    wrln("# Genotype format version 1.0")
+    wrln("# Individuals = "+str(num_inds))
+    wrln("# Phenotypes = "+str(len(num_snps)))
+
+    def out(i,x):
+        # print(i,x)
+        pass
         
-    snps = plink.readbed(options.geno+'.bed',num_inds, lambda i,x: print(i,x))
+    snps = plink.readbed(options.geno+'.bed',num_inds, out)
+    # for i in range(num_snps):
+    #     wr("\t"+str(i+1))
+    #     wr("\n")
+    # for i in range(count):
+    #     wr("\t".join(phenos[i]))
+    #     wr("\n")
     msg(str(count)+" geno lines written (with "+str(snps)+" snps)")
    
 msg("Converting done")
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/plink.py b/wqflask/wqflask/my_pylmm/pyLMM/plink.py
index 75d51c3b..4ad2c5f7 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/plink.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/plink.py
@@ -47,6 +47,8 @@ def readbim(fn):
         list = line.split()
         if len([True for e in list if e == 'nan']) == 0:
           res.append( (list[0],list[1],int(list[2]),int(list[3]),int(list[4]),int(list[5])) )
+        else:
+          res.append( (list[0],list[1],list[2],float('nan'),float('nan'),float('nan')) )
     return res
 
 # .bed (PLINK binary biallelic genotype table)
-- 
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