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Delete read_data.py

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HarshitGupta11 2019-07-24 15:56:33 +05:30 committed by GitHub
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read_data.py
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import os
import pandas as pd
import gzip
import sys
def clear_data(x):
x=x.split()
try:
x=x[1]
except:
c=0
#print(x)
x=x[1:-1]
return x
def read_data_genome(dir_name,a,dict_ind_genome):
lf=os.listdir(dir_name)
if len(lf)==0:
print("No files in the data directory!!!!!!")
sys.exit(1)
for x in lf:
data_gene=pd.read_csv(dir_name+"/"+x,compression='gzip',sep='\t',comment='#',header=None)
#print(data_gene.head)
data_gene=data_gene[data_gene[2]=="gene"]
data_gene=data_gene.sort_values(3)
tmp=data_gene[8].str.split(";",expand=True)
tmp=tmp.iloc[:,:5]
data_gene[["gene_id","gene_version","gene_name","gene_source","gene_biotype"]]=tmp
data_gene=data_gene.drop(8,axis=1)
#print(data_gene[0:10])
for y in ["gene_version","gene_name","gene_source","gene_biotype","gene_id"]:
data_gene[y]=data_gene[y].apply(clear_data)
#print(data_gene[0:10])
data_gene=data_gene[data_gene['gene_biotype']=='protein_coding']
a.append(data_gene)
n=x.split(".")[0]
dict_ind_genome[n]=len(a)-1
return a,dict_ind_genome
def read_data_homology(dir,a_h,d_h):
lf=os.listdir(dir)
if len(lf)==0:
print("No Files in the Directory!!!!!!!")
sys.exit(1)
for x in lf:
data=pd.read_csv(dir+"/"+x,compression='gzip',sep='\t')
a_h.append(data)
n=x.split(".")[0]
d_h[n]=len(a_h)-1
return a_h,d_h