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Removed Errors in Reading FastA Files

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HarshitGupta11 2019-06-05 13:51:31 +05:30 committed by GitHub
parent 0ec99556d1
commit d0e320059a
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1 changed files with 8 additions and 6 deletions
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14
read_get_gene_seq.py
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@ -95,12 +95,14 @@ def read_gene_sequences(df,lsy,data_dir,fname):
if gxr not in gene_by_species_dict[species]: if gxr not in gene_by_species_dict[species]:
gene_by_species_dict[species].append(gxr) gene_by_species_dict[species].append(gxr)
s=[x for x in gene_by_species_dict if len(gene_by_species_dict[x])!=0]#select those species only whose gene sequences we have to read. s=[x for x in gene_by_species_dict if len(gene_by_species_dict[x])!=0]#select those species only whose gene sequences we have to read.
s=[x.capitalize() for x in s] s=[x.capitalize() for x in s]
data=read_gene_seq(data_dir,s,gene_by_species_dict) print(len(s))
with open("processed/"+fname+".json","w") as file:#save the data data=read_gene_seq(data_dir,s,gene_by_species_dict)
json.dump(data,file)
return data with open("processed/"+fname+".json","w") as file:#save the data
json.dump(data,file)
return data