#!/usr/bin/env python
# coding: utf-8

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import pandas as pd


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import os


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from tqdm import tqdm


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#!cat /cellar/users/btsui/Data/ucsc_chains_human_homo_snps/hg38ToMm10.over.chain.gz.human_homo.bed | head


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liftOverDir='/cellar/users/btsui/Data/ucsc_chains_human_homo_snps/'


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fnames=pd.Series(os.listdir(liftOverDir))
inFnameS=fnames[~fnames.str.contains('unmapped')]


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myDict={}
for fname in tqdm(inFnameS):
    liftOverFDir=liftOverDir+fname
    liftUnmappedDir=liftOverFDir.replace('.human_homo.bed','.human_homo.unmapped.bed')

    #os.listdir(liftOverDir)

    colOrder=['Chr','Start','End','Rs']

    liftOverDf=pd.read_csv(liftOverFDir,sep='\t',header=None,)

    liftOverDf.columns=colOrder

    #unmappedS=pd.read_csv(liftUnmappedDir,header=None,)[0]

    #unmappedDf=unmappedS[(unmappedS.index%2)==1].str.split('\t',expand=True)

    #unmappedDf.columns=colOrder
    #mapped=liftOverDf.groupby('Chr').size().sum()
    myDict[fname ]=liftOverDf.shape[0]
    
    #print (total)


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unmappedS=pd.read_csv(liftUnmappedDir,header=None,)[0]

unmappedDf=unmappedS[(unmappedS.index%2)==1].str.split('\t',expand=True)

unmappedDf.columns=colOrder
mapped=liftOverDf.groupby('Chr').size().sum()


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total=liftOverDf.groupby('Chr').size().sum()+unmappedDf.groupby('Chr').size().sum()


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#liftOverDf


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tmpDf=(pd.Series(myDict)).reset_index()
tmpDf.columns=['Ucsc Chain Filename','Number of Human Snps Lifted Over']
#.sort_values(ascending=False).to_frame(name='PercentLiftedOver')


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tmpDf['Percent of Human Snps Lifted Over']=tmpDf['Number of Human Snps Lifted Over']/total


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ucscChainEfficiency=tmpDf.sort_values('Number of Human Snps Lifted Over',ascending=False)


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#!ls


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ucscChainEfficiency.to_csv('./Data/Human_Snps_Lifted_Over_efficiency.csv',index=False)


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#!head ./Data/Human_Snps_Lifted_Over_efficiency.csv


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unmappedDf.head()


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get_ipython().system('head $liftUnmappedDir')


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liftOverDf.columns=['']


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liftOverDf.head()


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#!ls -laht /cellar/users/btsui/Data/ucsc_chains_human_homo_snps/


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#!ls -lah /cellar/users/btsui/Data/ucsc_chains_human_homo_snps/hg38ToMm10.over.chain.gz.human_homo.bed


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pd.read_csv('/cellar/users/btsui/Data/ucsc_chains_human_homo_snps/hg38ToMm10.over.chain.gz.human_homo.bed',sep='\t',header=None)


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