KEGGTools | A collection of tools to download and process KEGG database | Database library

 by   FlyPythons Python Version: Current License: MIT

kandi X-RAY | KEGGTools Summary

kandi X-RAY | KEGGTools Summary

KEGGTools is a Python library typically used in Database applications. KEGGTools has no bugs, it has no vulnerabilities, it has a Permissive License and it has low support. However KEGGTools build file is not available. You can download it from GitHub.

KEGG is an important database to research on the function of proteins and metabolic pathways of certain organism, but the sequences in KEGG databases can not be downloaded free. KEGGTools is developed to solve this problem.
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            kandi-support Support

              KEGGTools has a low active ecosystem.
              It has 14 star(s) with 0 fork(s). There are no watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 1 open issues and 0 have been closed. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of KEGGTools is current.

            kandi-Quality Quality

              KEGGTools has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              KEGGTools is licensed under the MIT License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              KEGGTools releases are not available. You will need to build from source code and install.
              KEGGTools has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions, examples and code snippets are available.
              It has 708 lines of code, 46 functions and 10 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed KEGGTools and discovered the below as its top functions. This is intended to give you an instant insight into KEGGTools implemented functionality, and help decide if they suit your requirements.
            • Process protos
            • Check file format
            • Open a FASTA file
            • Process a protein
            • Convert KEGG Organisms to taxon ranks
            • Read a KEGG organization file
            • Read taxon from file
            • Concatenate protein and keg files
            • Reads the logo file
            • Read a kegg result file
            • Read a table from a file
            • Plot a KEGG annotation result
            • Read organism infomation from file
            • Output a kegg map to a file
            • Download a set of organizations
            • Download proteins from an organization
            • Parse a kegg map file
            • Convert KEGG org to org list
            • Set the command line arguments
            Get all kandi verified functions for this library.

            KEGGTools Key Features

            No Key Features are available at this moment for KEGGTools.

            KEGGTools Examples and Code Snippets

            No Code Snippets are available at this moment for KEGGTools.

            Community Discussions

            QUESTION

            How to create or alter a DB schema dynamically (at run time) using Gramex FormHandler
            Asked 2022-Apr-08 at 06:35

            I want to be able to (at run time) create or alter a DB schema dynamically on a particular event (e.g. click of a button) using FormHandler microservice of Gramex.

            ...

            ANSWER

            Answered 2022-Apr-08 at 06:20

            You can do it using queryfunction of FormHandler which can modify the query based on the query parameters passed in the url.

            Refer the link below for more https://gramener.com/gramex/guide/formhandler/#formhandler-queryfunction

            Source https://stackoverflow.com/questions/71792397

            QUESTION

            What does stopping the runtime while uploading a dataset to Hub cause?
            Asked 2022-Mar-24 at 01:06

            I am getting the following error while trying to upload a dataset to Hub (dataset format for AI) S3SetError: Connection was closed before we received a valid response from endpoint URL: "<...>".

            So, I tried to delete the dataset and it is throwing this error below.

            CorruptedMetaError: 'boxes/tensor_meta.json' and 'boxes/chunks_index/unsharded' have a record of different numbers of samples. Got 0 and 6103 respectively.

            Using Hub version: v2.3.1

            ...

            ANSWER

            Answered 2022-Mar-24 at 01:06

            Seems like when you were uploading the dataset the runtime got interrupted which led to the corruption of the data you were trying to upload. Using force=True while deleting should allow you to delete it.

            For more information feel free to check out the Hub API basics docs for details on how to delete datasets in Hub.

            If you stop uploading a Hub dataset midway through your dataset will be only partially uploaded to Hub. So, you will need to restart the upload. If you would like to re-create the dataset, you can use the overwrite = True flag in hub.empty(overwrite = True). If you are making updates to an existing dataset, you should use version control to checkpoint the states that are in good shape.

            Source https://stackoverflow.com/questions/71595867

            QUESTION

            MongoDB query all documents contains ids that does not exist anymore in the collection
            Asked 2022-Mar-02 at 03:10

            I ran into an issue that I haven't found a solution to yet. I have a collection with dozens of documents that every one of the documents contains a list (let's use the name 'list' as a key for that list) with ids of other documents(they are connected in some way).

            some of the documents in the collection were deleted and I try to find all the documents that contain the ids of documents that do not exist anymore in the collection.

            example:

            As to the example above: I want to get the document with the id : 5e3266e9bd724a000107a902 because it contains a list with the id 5e32a7f7bd724a00012c1104 that does not exist anymore.

            ...

            ANSWER

            Answered 2022-Mar-02 at 03:10

            Here is a solution that works exploiting $lookup on the same collection (think "self-JOIN"):

            Source https://stackoverflow.com/questions/71313345

            QUESTION

            Is it possible to change the active user for a PostgreSQL connection?
            Asked 2022-Mar-02 at 02:49

            Given a connection to the PostgreSQL database for user 'Alice', is there a statement that could be executed to switch to user 'Bob'?

            Motivation: Looking to avoid having separate pools for each user (i.e. re-use a connection that was previously used by another user).

            ...

            ANSWER

            Answered 2022-Mar-01 at 22:09

            In PgAdmin open part Login/Group roles. Right click and in opened window enter new user, set permission and defined password. After refresh you will see e.g. Alice in Login/Group roles. After that open database with logged user. Click on something like mondial/postgres@PostgresSQL (db/user@server) and choose new connection. Chose which db wish to use and user wich will be connected on db.

            After that you will have mondial/Alice@PostgresSQL

            Source https://stackoverflow.com/questions/71315070

            QUESTION

            null is not an object Sqlite + ReactNative expo Typescript
            Asked 2022-Feb-28 at 12:43

            I made login page and now i'm trying to replace simple user.js to Sqlite Database (react-native-sqlite-storage). When i launch my project with database, i get this error.

            My Code

            ...

            ANSWER

            Answered 2022-Feb-28 at 12:43

            The problem consist from creating connection in separate file (must be create in App).

            Source https://stackoverflow.com/questions/71282268

            QUESTION

            Indexing for GROUP BY in CosmosDB
            Asked 2022-Feb-28 at 09:33

            As the title suggests I'm wondering how to create an effective index for GROUP BY queries in CosmosDB.

            Say the documents look something like:

            ...

            ANSWER

            Answered 2021-Sep-27 at 20:51

            Currently GROUP BY does not not yet use the index.

            This is currently being worked on. I would revisit sometime towards the end of the year to verify it is supported.

            Source https://stackoverflow.com/questions/69348335

            QUESTION

            Is there a way to implement cassandra "decimal" Datatype in Golang
            Asked 2022-Feb-15 at 12:13

            i have a database field that is set to decimal, while in my Go project i am having problem choosing which datatype can be use. each time i send a create reuquest to my code, i get a "cannot marshal 'decimal' into #golang datatype#

            this my database schema

            ...

            ANSWER

            Answered 2022-Feb-15 at 12:13

            If you look into documentation for Gocql package, then you will see that the decimal is mapped to the Go's infDec data type (see its doc) so you need to use it instead of Float64.

            Source https://stackoverflow.com/questions/71125652

            QUESTION

            How do I copy a big database table to another in ABAP?
            Asked 2022-Feb-03 at 09:29

            I want to copy one big database table to another. This is my current approach:

            ...

            ANSWER

            Answered 2022-Jan-20 at 12:45

            You can also "copy on database level" from within ABAP SQL using a combined INSERT and SELECT:

            Source https://stackoverflow.com/questions/70763128

            QUESTION

            Upgrade H2 version 2.0.202 from 1.4.200
            Asked 2022-Jan-31 at 01:05
            1. Hi, we are trying to upgrade 2.0.202 from 1.4.200. We are getting an error related to running our tests. While persisting data we are getting below error. Any suggestions?

            Caused by: org.h2.jdbc.JdbcSQLIntegrityConstraintViolationException: NULL not allowed for column "***"; SQL statement:

            ...

            ANSWER

            Answered 2022-Jan-31 at 01:05

            You cannot use H2 2.0.202 with Hibernate ORM 5.6, because H2Dialect in Hibernate ORM produces invalid SQL for H2, H2 2.x is more restrictive and doesn't accept it by default.

            H2 2.0.204 and later versions (current version is 2.1.210) have a LEGACY compatibility mode, it can be enabled by appending ;MODE=LEGACY to JDBC URL. This mode provides some limited compatibility with old versions of H2.

            This trick shouldn't be required for Hibernate ORM 6.0 when it will be released.

            Edited

            Changes for H2 2.x.y were backported to Hibernate ORM 5.6.5.

            Source https://stackoverflow.com/questions/70818631

            QUESTION

            What are the backend service for flutter?
            Asked 2022-Jan-29 at 13:44

            I am confused in choosing database service for my flutter application. I started using firebase but as it is based on NoSQL , But if i am getting the need for rows and columns for my data which backend service should i use!.

            ...

            ANSWER

            Answered 2022-Jan-23 at 23:20

            I think it depends on how you want to access the data. If you're wanting to stream and push notifications, I would stick with Firebase. If you just need to get and post data, focus more on api implementation. With a solid rest api, you can change up your database/backend all you want and just have to update the api, not your app.

            I, personally, suggest searching around for data modeling techniques in Firebase. Check out the Fireship channel on youtube. In his channel's videos, search for modeling and you'll find a ton of info on Firebase data modeling. Many will reference Angular, but the techniques are the same.

            Source https://stackoverflow.com/questions/70827265

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

            Vulnerabilities

            No vulnerabilities reported

            Install KEGGTools

            This will get 5426 KEGG organisms from KEGG-Genome. This will get 5419 gzip formatted protein sequences of KEGG organisms from NCBI. Other 7 organsims are not from NCBI, they are "bpg dosa lem lja pfd pfh smin" 3. Download KO information from KEGG. This will get 5394 keg formatted file consist KO information of KEGG organisms. Other 32 organisms have no KO information in KEGG, they are "ebc pcd apor pgz vta cola haf mii aea nmj bgm aon kso zpa afq amih ypac mee msao dpc rhq dlu cgrn sfk actt pbf kst vbh fmo ful pbp dod " 4. Get proteins included in KO files from NCBI download proteins. This will get protein sequences of 5381 organisms. 13 of organsims can not find matched id in KEGG-KO and NCBI-protein, they are "agl cpor pary smiz pshi tng vrm dpl dco hlc ecor nwe xph"; 32 organisms have no KO information in KEGG, they are present in step 4. So finally, we have a KEGG database consist 5381 organisms, we can use them to do KEGG annotation.
            Download information of KEGG organisms from KEGG
            Download protein sequences from NCBI by the urls in 'KEGG.org'

            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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            https://github.com/FlyPythons/KEGGTools.git

          • CLI

            gh repo clone FlyPythons/KEGGTools

          • sshUrl

            git@github.com:FlyPythons/KEGGTools.git

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