I am trying to work on Uniprot directly from my jupyter notebook. My search keywords are TERM "tumor+necrosis+factor+receptor" and ORGANISM "Homo sapiens".
Here's how far I have succeeded
import requests BASE = 'http://www.uniprot.org' KB_ENDPOINT = '/uniprot/' TOOL_ENDPOINT = '/uploadlists/' fullURL = ('http://www.uniprot.org/uniprot/?' 'query=name%3A%22tumor+necrosis+factor+receptor%22+AND+taxonomy%3Ahuman+AND+reviewed%3Ayes&' 'format=list') result = requests.get(fullURL) if result.ok: print(result.text) else: print('Something went wrong ', result.status_code)
This gives me only partial list of proteins.the actual search on uniprot gives over 400 entries.
Any idea what went wrong?
Hi!
Did you try to work with bioservices?
Here is the example:
https://nbviewer.ipython.org/github/cokelaer/bioservices/blob/master/doc/notebooks/UniProt.ipynb
Would there be an option to fetch multiple FASTA sequences in a single instance?@Timur Yergaliyev
Timur Yergaliyev Also, when I install Bioservices on my jupyter notebook, it says requirement satisfied. However, when I try to import uniprot from Bioservices, it returns the module not found error. I've installed the dependencies for Bioservices, but I don't know what's going on? I'm completely new to Python and would really appreciate any guidance.
Thanks,
Hrshita
Hrshita Gowda Yes, use batch retrieval from Uniprot API.
follow this https://www.uniprot.org/help/api_idmapping
import urllib.parse import urllib.request url = 'https://www.uniprot.org/uploadlists/' params = { 'from': 'ACC+ID', 'to': 'ENSEMBL_ID', 'format': 'tab', 'query': 'P40925 P40926 O43175 Q9UM73 P97793' } data = urllib.parse.urlencode(params) data = data.encode('utf-8') req = urllib.request.Request(url, data) with urllib.request.urlopen(req) as f: response = f.read() print(response.decode('utf-8'))
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