specie='Homo_sapiens'
snpBed='/cellar/users/btsui/Data/dbsnp/snp_beds/'+specie+'.bed'
import pandas as pd
tmpDf=pd.read_csv(snpBed,sep='\t',header=None)
/cellar/users/btsui/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py:2785: DtypeWarning: Columns (0) have mixed types. Specify dtype option on import or set low_memory=False. interactivity=interactivity, compiler=compiler, result=result)
tmpDf[0]='chr'+tmpDf[0].astype(str)
'/cellar/users/btsui/Data/dbsnp/snp_beds/Homo_sapiens.bed'
tmpDf.to_csv(snpBed+'.with_chr',sep='\t',header=None,index=None)
!head /cellar/users/btsui/Data/dbsnp/snp_beds/Homo_sapiens.bed.with_chr
chr1 14727 14727 chr1 630825 630825 chr1 630833 630833 chr1 817186 817186 chr1 833068 833068 chr1 842133 842133 chr1 843942 843942 chr1 850609 850609 chr1 948136 948136 chr1 955964 955964
## the dbsnp contains all the reference bases