Protein molar mass from Uniprot ID?

Question

I have a long list of uniprot IDs. How can I get the mass of the "canonical" isoform for each? Ideally from some Python library.

Answer 1

You don't need any external library, it's enough to query Uniprot and extract the data you want from the response.

Here an example in Python 3:

from urllib.request import urlopen

id = "P42212"
data = urlopen("http://www.uniprot.org/uniprot/" + id + ".txt").read().decode()
result = data.split('SQ   ')[-1] #here all the info you need
mw = int(result.split(';')[1].strip().split()[0]) #extract the molecular weigth
print(mw)

If you want to batch query a lot of sequences then I suggest to sleep(0.5) after each query to avoid problems with their server.

Update

As correctly pointed out by @Jerven (see comment below), you can query the mass directly.

In this case, the code is the following:

from urllib.request import urlopen

id = "P42212"
data = urlopen("http://www.uniprot.org/uniprot/?query=id:{}&format=tab&columns=id,mass".format(id)).read().decode()
result = data.split('\n')[1].replace(',','')
mw = int(result.split('\t')[-1])
print(mw)