mirror of
https://github.com/Priyatham-sai-chand/compara-deep-learning.git
synced 2026-10-05 08:11:34 -07:00
38 lines
1.1 KiB
Python
38 lines
1.1 KiB
Python
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])
|
|
a.append(data_gene)
|
|
n=x.split(".")[0]
|
|
dict_ind_genome[n]=len(a)-1
|
|
return a,dict_ind_genome
|