--- a/vcf_snp.py	Mon Nov 02 19:42:54 2015 -0500
+++ b/vcf_snp.py	Fri Nov 06 15:12:17 2015 -0500
@@ -1,13 +1,14 @@
 #!/usr/bin/env python
+##!/usr/local/anaconda/bin/python
 
 #########################################################################################
 #											#
 # Name	      :	vcf_snp.py								#
-# Version     : 0.2									#
+# Version     : 0.3									#
 # Project     : extract snp from vcf						#
 # Description : Script to exctract snps		#
 # Author      : Brigida Rusconi								#
-# Date        : November 02 2015							#
+# Date        : November 06 2015							#
 #											#
 #########################################################################################
 
@@ -30,40 +31,54 @@
 
 parser.add_argument('-o', '--output', help="snp tab")
 parser.add_argument('-s', '--snp_table', help="vcf")
+parser.add_argument('-p', '--positions', help="positions")
+
 
 
 args = parser.parse_args()
 output_file = args.output
 input_file = args.snp_table
+input_file2=args.positions
 #------------------------------------------------------------------------------------------
 
 
 #read in file as dataframe
 df =read_csv(input_file,sep='\t', dtype=object)
+df3=read_csv(input_file2,sep='\t', dtype=object, names=['#CHROM','POS'])
+#pdb.set_trace()
+#get the positions that are missing
+if df.index.size!= df3.index.size:
+    df4=df3[~df3.POS.isin(df.POS)]
+#pdb.set_trace()
+    df4=df4.set_index('POS')
+    df=df.set_index('POS')
+    df2=concat([df,df4], axis=1)
+#if there is no information for a loci the position is dropped so it fills the nan with N
+    df5=df2.iloc[:, 2:4].fillna('N')
+    df5=df5.reindex(df3.POS)
+else:
+    df5=df.iloc[:,3:5]
 
 #------------------------------------------------------------------------------------------
 
-# only columns with qbase and refbase in table
-#count_qbase=list(df.columns.values)
-#qindexes=[]
-#for i, v in enumerate(count_qbase):
-#    if 'ALT' in v:
-#        qindexes.append(i)
-df2=df.iloc[:,3:5]
+
 #pdb.set_trace()
 
 #------------------------------------------------------------------------------------------
+#replaces the . with the nucleotide call of the reference also deals with multiallelic states calling them N
 ref_list=[]
-for i in range(0,df2.index.size):
-    if df2.iloc[i,1]==".":
-        ref_list.append(df2.iloc[i,0][0])
+for i in range(0,df5.index.size):
+    if df5.iloc[i,1]==".":
+        ref_list.append(df5.iloc[i,0][0])
+    elif len(df5.iloc[i,1])>1:
+        ref_list.append('N')
     else:
-        ref_list.append(df2.iloc[i,1][0])
+        ref_list.append(df5.iloc[i,1][0])
 #pdb.set_trace()
 #
 ##------------------------------------------------------------------------------------------
 #
 #save file with output name for fasta -o option and removes header and index
 with open(output_file,'w') as output:
-    output.write(df.columns.values[4] + '\t' + ''.join([str(i) for v,i in enumerate(ref_list)]))
+    output.write('ALT' + '\t' + ''.join([str(i) for v,i in enumerate(ref_list)]))
 ##------------------------------------------------------------------------------------------
\ No newline at end of file