lorenapr92

import sys

infile = 'chr7first300.vcf'

class ParseV:

    def __init__(self,infile,List=None,samplestuff=None):
        self.infile = infile
        self.List = []
        self.samplestuff=[] # creates a new empty list, think this addresses the problem from last time where the mistaken use of class variable with a mutable data type?

lorenapr92

#This will parse out the SNPs from chr 7 Foxp2 gene into a vcf file, from phase 3 1000 genomes project, all subjects genome build 37
#Jennifer Owen
#Stephanie Perez Robles
#Lisa Dimusto
import sys

infile = 'ALL.chr7.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf'

class ParseV:

lorenapr92

#This will parse out the SNPs from chr 6 KIAA0319 gene into a vcf file, from phase 3 1000 genomes project, all subjects genome build 37
#Jennifer Owen
#Stephanie Perez Robles
#Lisa Dimusto
import sys

infile = 'ALL.chr6.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf'

class ParseV:

lorenapr92

#This will parse out the SNPs from chr 7 CNTNAP2 gene into a vcf file, from phase 3 1000 genomes project, all subjects genome build 37
#Jennifer Owen
#Stephanie Perez Robles
#Lisa Dimusto
import sys

infile = 'ALL.chr7.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf'

class ParseV:

lorenapr92

#This code will convert sequences into amino acids by using the gencode table below.
#Jennifer Owen
#Stephanie Perez
#Lisa DiMusto



import sys
import re