uniprot | retrieve protein sequence identifiers and metadata | Genomics library

 by   boscoh Python Version: 1.3 License: No License

kandi X-RAY | uniprot Summary

kandi X-RAY | uniprot Summary

uniprot is a Python library typically used in Artificial Intelligence, Genomics applications. uniprot has no bugs, it has no vulnerabilities, it has build file available and it has low support. You can install using 'pip install uniprot' or download it from GitHub, PyPI.

uniprot.py provides a Python interface to the UniProt website to:.
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            kandi-support Support

              uniprot has a low active ecosystem.
              It has 47 star(s) with 12 fork(s). There are 8 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 1 open issues and 2 have been closed. On average issues are closed in 122 days. There are 1 open pull requests and 0 closed requests.
              It has a neutral sentiment in the developer community.
              The latest version of uniprot is 1.3

            kandi-Quality Quality

              uniprot has 0 bugs and 0 code smells.

            kandi-Security Security

              uniprot has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.
              uniprot code analysis shows 0 unresolved vulnerabilities.
              There are 0 security hotspots that need review.

            kandi-License License

              uniprot does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              uniprot releases are not available. You will need to build from source code and install.
              Deployable package is available in PyPI.
              Build file is available. You can build the component from source.
              Installation instructions, examples and code snippets are available.
              uniprot saves you 247 person hours of effort in developing the same functionality from scratch.
              It has 600 lines of code, 27 functions and 3 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed uniprot and discovered the below as its top functions. This is intended to give you an instant insight into uniprot implemented functionality, and help decide if they suit your requirements.
            • 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
            Get all kandi verified functions for this library.

            uniprot Key Features

            No Key Features are available at this moment for uniprot.

            uniprot Examples and Code Snippets

            UNIPROT.PY,Examples,Brute-force seqid-type matching
            Pythondot img1Lines of Code : 17dot img1no licencesLicense : No License
            copy iconCopy
            >> 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  
            UNIPROT.PY,Chaining calls
            Pythondot img2Lines of Code : 11dot img2no licencesLicense : No License
            copy iconCopy
            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.PY,Examples,Getting protein sequence metadata
            Pythondot img3Lines of Code : 7dot img3no licencesLicense : No License
            copy iconCopy
            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

            QUESTION

            How do I make a python dictionary from a string?
            Asked 2021-Jun-05 at 06:12

            I am collecting protein sequence ids from this website: https://www.uniprot.org/

            I've written this code:

            ...

            ANSWER

            Answered 2021-Jun-05 at 06:04

            Basically, just appropriately split and use the values in the string. The code is as follows:

            Source https://stackoverflow.com/questions/67839843

            QUESTION

            Creating a SPARQL query that extracts information out of a `rdf:Bag` without loss of information
            Asked 2021-Apr-11 at 16:58

            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 16:58
            SELECT ?x (bqbiol:is AS ?y) ?z {
                ?x bqbiol:is [ a rdf:Bag ; !a ?z ] . 
            }
            

            Source https://stackoverflow.com/questions/67020626

            QUESTION

            Conversion of a webpage to text
            Asked 2021-Feb-18 at 20:12

            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 03:30

            Use 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.

            Source https://stackoverflow.com/questions/66253079

            QUESTION

            searching file using re.search and saving output to new file
            Asked 2021-Jan-29 at 10:54

            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 10:51

            QUESTION

            How to convert list to table using Python?
            Asked 2021-Jan-25 at 13:53

            I have the list which contains 50 sample IDs. The part of the list looks like the following:

            ...

            ANSWER

            Answered 2021-Jan-25 at 13:30

            Supposed you have your addToTable method which takes a query and a name then you can do the following:

            Source https://stackoverflow.com/questions/65885190

            QUESTION

            Python Beautiful Soup html.parser returns none
            Asked 2021-Jan-22 at 07:47

            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 04:20

            There 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.

            Source https://stackoverflow.com/questions/65821009

            QUESTION

            Is it possible to identify an item in a json dictionary's list, without hard-coding the list position?
            Asked 2021-Jan-18 at 13:31

            I have this json dict:

            ...

            ANSWER

            Answered 2021-Jan-18 at 13:31

            You can use the following. It will print the desired output, no matter the position of the dict inside the list.

            Source https://stackoverflow.com/questions/65775023

            QUESTION

            Retrieve many nested statements at the same time for a single object with lxml Python
            Asked 2020-Oct-30 at 16:12

            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 16:12

            Here is a slightly alternative approach:

            Source https://stackoverflow.com/questions/64606363

            QUESTION

            Getting protein sequences by accessing Uniprot (with Python)
            Asked 2020-Sep-21 at 13:18

            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)

            Source https://stackoverflow.com/questions/63992865

            QUESTION

            Performing a function on a set of protein sequences, would like to make it that my output will also include the name of sequence from a dictionary
            Asked 2020-Aug-31 at 12:16
            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 12:16

            I 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:

            Source https://stackoverflow.com/questions/63660803

            Community Discussions, Code Snippets contain sources that include Stack Exchange Network

            Vulnerabilities

            No vulnerabilities reported

            Install uniprot

            If you're installing directly from setup.py, be aware that uniprot.py has one dependency: requests.py:.

            Support

            For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .
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            pip install uniprot

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            gh repo clone boscoh/uniprot

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            git@github.com:boscoh/uniprot.git

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