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#This code will convert sequences into amino acids by using the gencode table below. | |
#Jennifer Owen | |
#Stephanie Perez | |
#Lisa DiMusto | |
import sys | |
import re |
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#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: |
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#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: |
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#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: |
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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? |