2019-05-10 10:21:21 -07:00
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import os
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import pandas as pd
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import gzip
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import sys
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def clear_data(x):
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x=x.split()
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try:
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x=x[1]
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except:
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c=0
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#print(x)
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x=x[1:-1]
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return x
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def read_data_genome(dir_name,a,dict_ind_genome):
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lf=os.listdir(dir_name)
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if len(lf)==0:
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print("No files in the data directory!!!!!!")
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sys.exit(1)
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for x in lf:
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data_gene=pd.read_csv(dir_name+"/"+x,compression='gzip',sep='\t',comment='#',header=None)
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#print(data_gene.head)
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data_gene=data_gene[data_gene[2]=="gene"]
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data_gene=data_gene.sort_values(3)
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tmp=data_gene[8].str.split(";",expand=True)
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tmp=tmp.iloc[:,:5]
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data_gene[["gene_id","gene_version","gene_name","gene_source","gene_biotype"]]=tmp
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data_gene=data_gene.drop(8,axis=1)
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#print(data_gene[0:10])
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for y in ["gene_version","gene_name","gene_source","gene_biotype","gene_id"]:
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data_gene[y]=data_gene[y].apply(clear_data)
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2019-05-10 10:33:34 -07:00
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#print(data_gene[0:10])
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2019-05-10 10:21:21 -07:00
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a.append(data_gene)
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n=x.split(".")[0]
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dict_ind_genome[n]=len(a)-1
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return a,dict_ind_genome
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2019-05-11 11:22:42 -07:00
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def read_data_homology(dir,a_h,d_h):
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lf=os.listdir(dir)
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if len(lf)==0:
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print("No Files in the Directory!!!!!!!")
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sys.exit(1)
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for x in lf:
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data=pd.read_csv(dir+"/"+x,compression='gzip',sep='\t')
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a_h.append(data)
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n=x.split(".")[0]
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d_h[n]=len(a_h)-1
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return a_h,d_h
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