uniprot | retrieve protein sequence identifiers and metadata | Genomics library
kandi X-RAY | uniprot Summary
kandi X-RAY | uniprot Summary
uniprot.py provides a Python interface to the UniProt website to:.
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Top functions reviewed by kandi - BETA
- Parse isoformats
- Get uniprot metadata for given seqids
- Get metadata for a list of sequences
- Batch mapping a sequence of sequences to another
- Fetch metadata from UniProt IDs
- Parse the UniProt metadata for the given seqids
- Clean a list of sequences
- Generate metadata for a list of unique sequences
- Parse isoform data into a dict
- Batch a sequence of sequences mapped to another
- Read a FASTA file from a fasta database
- Parse a fasta header from a fasta file
- Parse UniProt metadata with given sequences
- Read protein sequences from a fasta database
- Get filtered uniprot metadata
- Return True if seqid is a UniProt sequence
- Test if seqid is a refseq
- Returns True if seqid is a SGD
uniprot Key Features
uniprot Examples and Code Snippets
>> seqidtype YP_885981.1
===> Analyzing YP_885981.1
Fetching 1 (ACC->ACC) seqid mappings ...
YP_885981.1 -> ACC -> None
Fetching 1 (ID->ACC) seqid mappings ...
YP_885981.1 -> ID -> None
.
.
.
Fetching 1 (P_REFSEQ_AC->A
metadata = uniprot.get_metadata_with_some_seqid_conversions(
seqids, 'cache')
# convert a few types into uniprot_ids
id_types = [
(is_sgd, 'locustag', 'ENSEMBLGENOME_PRO_ID'),
(is_refseq, 'refseqp', 'P_REFSEQ_AC'),
(is_refseq, 'refseqnt',
uniprot_seqids = 'A0QSU3 D9QCH6 A0QL36'.split()
uniprot_data = uniprot.batch_uniprot_metadata(
uniprot_seqids, 'cache')
pprint.pprint(mapping, indent=2)
uniprot.write_fasta('output.fasta', uniprot_data, uniprot_seqids)
for l in open('cache/meta
Community Discussions
Trending Discussions on uniprot
QUESTION
I am collecting protein sequence ids from this website: https://www.uniprot.org/
I've written this code:
...ANSWER
Answered 2021-Jun-05 at 06:04Basically, just appropriately split and use the values in the string. The code is as follows:
QUESTION
I'm pretty new to RDF, but I need to construct an RDF query to extract some information from an existing RDF graph. In essence, I'm trying to purge existing RDF graphs of the rdf:Bag
construct.
For instance, given the RDF graph:
...ANSWER
Answered 2021-Apr-11 at 16:58SELECT ?x (bqbiol:is AS ?y) ?z {
?x bqbiol:is [ a rdf:Bag ; !a ?z ] .
}
QUESTION
I was trying to convert a webpage to text and save it in a txtfile. I coded the following scripts in python. It is working but the text quality is not workable.
Is there any way the text file would be of much better quality and meaning could be realized.
Here's my code:
...ANSWER
Answered 2021-Feb-18 at 03:30Use the BeautifulSoup
library together with the requests
library will get you at least to a good start. Once you study the first library some more, you might be able to customize your program to extract only the text you want. See below.
Also, please see here for a similar question: Text Extracting: Used All Methods, Yet Stuck.
QUESTION
I have been wrestling with this for some time now:
I am searching a file for a pattern and want to save the output to another file. However I keep getting the error:
...ANSWER
Answered 2021-Jan-29 at 10:51This
QUESTION
I have the list which contains 50 sample IDs. The part of the list looks like the following:
...ANSWER
Answered 2021-Jan-25 at 13:30Supposed you have your addToTable
method which takes a query and a name then you can do the following:
QUESTION
I have a feeling the information is somewhere on stack overflow, but I can't find it :-/
I'm looking to get the text from this website: https://www.uniprot.org/uniprot/P28653.fasta but my code returns 'None.' All help is super appreciated!
...ANSWER
Answered 2021-Jan-21 at 04:20There is no html in the site. You can just print r.content
directly (however, I prefer r.text
as it is a string
not a bytes
object) , and it will contain the string on the page. Remember, when you use developer tools in chrome (or other browsers), the html you see when you inspect is not necessarily the same result that requests will get. Usually viewing the source code directly in your browser (or printing out the result of requests.get(url).text/.content
) will give a more accurate picture of what html you are dealing with.
QUESTION
I have this json dict:
...ANSWER
Answered 2021-Jan-18 at 13:31You can use the following. It will print the desired output, no matter the position of the dict inside the list.
QUESTION
I am working with big xml where I am retrieving many different properties, and now I am trying to retrieve comment category
property and connect it to the text between the tags. However, there are 3 different situations that I need to handle. XML example:
ANSWER
Answered 2020-Oct-30 at 16:12Here is a slightly alternative approach:
QUESTION
I have a list of protein id's I'm trying to access the protein sequences from Uniprot with python. I came across this post :Protein sequence from uniprot protein id python but gives a list of elements and not the actual sequence:
Code ...ANSWER
Answered 2020-Sep-21 at 13:18[record.seq for record in pSeq]
edit:
You'll want str(pSeq[0].seq)
QUESTION
Code:
Seq_List=open('test.trunc..txt','r')#uses tab files from uniprot copied into notepad 250 work
data = Seq_List.readlines()
N, P = [], []
for line in data:
values = [str(s) for s in line.split()]
N.append(values[0])
P.append(values[1])
N.remove('Entry')
P.remove('Sequence')
print(P)
Sequencedict = {}
for key in N:
for value in P:
Sequencedict[key] = value
#P.remove(value)
break
print(Sequencedict)
print(Sequencedict.values())
def idr (P):
for i in P:
x= i.replace('Q','e').replace('R','b').replace('S','e').replace('T','e').replace('Y','e')]
#print(x)#gives the converted sequences
#print(type(x))#output x is a list
for g in x:
v=g.count('h')
#print(v)
y=g.count('e')+g.count('a')+g.count('b')
#print(y)
z=len(i)
#print(values)
#print(y/z)
if y/z>.10: #and v/z<.10: #e/tot>.60=sumo
print(i)
print(Sequencedict.keys())#reprint i and swap based of dict
print(v)
print(y)
print(y/z)
print('Disorder Promoting=Yes')
#else:
#print('Disorder Promoting=No')
idr (P)
Output:
['MSRTIVALILLGLAALA', 'MARFLVALALFGVVAMTAA', 'MARLFVAVALFGVVAFAAAEK']
{'P0CU41': 'MSRTIVALILLGLAALA', 'P0CU39': 'MSRTIVALILLGLAALA', 'P0CU40': 'MSRTIVALILLGLAALA'}
dict_values(['MSRTIVALILLGLAALA', 'MSRTIVALILLGLAALA', 'MSRTIVALILLGLAALA'])
MSRTIVALILLGLAALA
dict_keys(['P0CU41', 'P0CU39', 'P0CU40'])
14
3
0.17647058823529413
Disorder Promoting=Yes
MARFLVALALFGVVAMTAA
dict_keys(['P0CU41', 'P0CU39', 'P0CU40'])
17
2
0.10526315789473684
Disorder Promoting=Yes
MARLFVAVALFGVVAFAAAEK
dict_keys(['P0CU41', 'P0CU39', 'P0CU40'])
18
3
0.14285714285714285
Disorder Promoting=Yes
...ANSWER
Answered 2020-Aug-31 at 12:16I think there are a few problems with your code. First I guess you want to combine the first key in your list N with the first value from your list P, next the second key from N with the second value from P and so on? The code you actually have does not do that. At the moment it just applies to every key, the first value of P. I would suggest to zip the values together:
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