I am trying to get the following script to work. The input file consists of 3 columns: gene association type, gene name, and disease name.
cols = ['Gene type', 'Gene name', 'Disorder name']
no_headers = pd.read_csv('orphanet_infoneeded.csv', sep=',',header=None,names=cols)
gene_type = no_headers.iloc[1:,[0]]
gene_name = no_headers.iloc[1:,[1]]
disease_name = no_headers.iloc[1:,[2]]
query = 'Disease-causing germline mutation(s) in' ###add query as required
orph_dict = {}
for x in gene_name:
if gene_name[x] in orph_dict:
if gene_type[x] == query:
orph_dict[gene_name[x]]=+ 1
else:
pass
else:
orph_dict[gene_name[x]] = 0
I keep getting an error that says:
Series objects are mutable and cannot be hashed
Any help would be dearly appreciated!
2 Answers
Shortly: gene_name[x] is a mutable object so it cannot be hashed. To use an object as a key in a dictionary, python needs to use its hash value, and that's why you get an error.
Further explanation:
Mutable objects are objects which value can be changed.
For example, list is a mutable object, since you can append to it. int is an immutable object, because you can't change it. When you do:
a = 5;
a = 3;
You don't change the value of a, you create a new object and make a point to its value.
Mutable objects cannot be hashed. See this answer.
To solve your problem, you should use immutable objects as keys in your dictionary. For example: tuple, string, int.
gene_name = no_headers.iloc[1:,[1]]
This creates a DataFrame because you passed a list of columns (single, but still a list). When you later do this:
gene_name[x]
you now have a Series object with a single value. You can't hash the Series.
The solution is to create Series from the start.
gene_type = no_headers.iloc[1:,0]
gene_name = no_headers.iloc[1:,1]
disease_name = no_headers.iloc[1:,2]
Also, where you have orph_dict[gene_name[x]] =+ 1, I'm guessing that's a typo and you really mean orph_dict[gene_name[x]] += 1 to increment the counter.
