entrez | simple Python interface to the amazing NCBI databases | Database library

 by   jordibc Python Version: Current License: GPL-3.0

kandi X-RAY | entrez Summary

kandi X-RAY | entrez Summary

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

A simple Python interface to query the biological databases kept at the NCBI. It uses the Entrez Programming Utilities (E-utilities), nine server-side programs that access the Entrez query and database system at the National Center for Biotechnology Information (NCBI).
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            kandi-support Support

              entrez has a low active ecosystem.
              It has 15 star(s) with 3 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              entrez has no issues reported. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of entrez is current.

            kandi-Quality Quality

              entrez has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              entrez is licensed under the GPL-3.0 License. This license is Strong Copyleft.
              Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

            kandi-Reuse Reuse

              entrez releases are not available. You will need to build from source code and install.
              entrez has no build file. You will be need to create the build yourself to build the component from source.
              Installation instructions are not available. Examples and code snippets are available.
              It has 259 lines of code, 21 functions and 4 files.
              It has low code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed entrez and discovered the below as its top functions. This is intended to give you an instant insight into entrez implemented functionality, and help decide if they suit your requirements.
            • Sample from database
            • Yield the results of a tool
            • Select the elements selected by the tool
            • Generate a list of SNPs
            • Returns a generator of the results of the eutils query
            • Example application
            • Search for a search term
            • Prints out duplicates
            • Parses the input raw data
            • Sample data
            • Search for a given term
            • Sample the database
            • Sample
            • Sample a single protein
            • Extract the amino acid sequence
            • Takes a sequence of accessions and converts to gene name
            • Reads the accessions from a list of files
            Get all kandi verified functions for this library.

            entrez Key Features

            No Key Features are available at this moment for entrez.

            entrez Examples and Code Snippets

            No Code Snippets are available at this moment for entrez.

            Community Discussions

            QUESTION

            Flutter Error: No named parameter with the name 'keyboardType'.keyboardType: TextInputType.text
            Asked 2022-Mar-31 at 10:42

            I am new on Flutter and I would like to set up a form. This is my code:

            ...

            ANSWER

            Answered 2021-Oct-06 at 09:51

            Try below code I think your problem has been solved. refer Textfield here

            Source https://stackoverflow.com/questions/69463211

            QUESTION

            Find common rows across multiple, but not all available data frames, for all possible combinations of all those data frames
            Asked 2022-Mar-30 at 19:26

            I have multiple data frames with the following format:

            ...

            ANSWER

            Answered 2022-Mar-30 at 19:26

            One option involving dplyr and purrr could be:

            Source https://stackoverflow.com/questions/71681932

            QUESTION

            Upgrading to pandas version 1.4.0 or 1.4.1 causes a call to the method .at[idx, "XXX"] to generate an InvalidIndexError
            Asked 2022-Mar-22 at 20:49

            my program fails after upgrading to python pandas version 1.4.0 or 1.4.1 with the following traceback :

            ...

            ANSWER

            Answered 2022-Mar-10 at 22:14

            Same error that could only be resolved by downgrading to pandas version 1.3.5, if you're using pip:

            Source https://stackoverflow.com/questions/71293357

            QUESTION

            Powershell Basic
            Asked 2022-Feb-28 at 16:03

            I have to do a simple calculator +, -, * and / on PowerShell for my coding introduction course. Why my Variable Valeur1 & Valeur2 don't remain intact during the integer validation ? My 4 options give a random answer and don't remember the initial value of my 2 Read-Host Variables.

            ...

            ANSWER

            Answered 2022-Feb-28 at 16:03

            From the Int32.TryParse(String, Int32) Documentation:

            result Int32
            When this method returns, contains the 32-bit signed integer value equivalent of the number contained in s, if the conversion succeeded, or zero if the conversion failed.

            When you do [ref]$OK, if the conversion succeeds, this variable will hold the parsed result of your .TryParse operation, but, you're overwriting this value on your if and else conditions ($OK = $true and $OK = $false).

            Furthermore, the output from the .TryParse method will be $true / $false depending on the success of the operation (this boolean will be assigned to $valeur1 and $valeur2 since both variables have assigned this operation).

            Returns Boolean
            true if s was converted successfully; otherwise, false.

            Here is a simplified, working, variation of your code. It's worth mentioning that, since you're performing 2 parse operations, a function (ParseInput) holding the same logic would make more sense so that the code is not repeated.

            Source https://stackoverflow.com/questions/71289661

            QUESTION

            R: How do I reduce the ranges of genes into a single vector?
            Asked 2022-Feb-19 at 23:15

            I created var_nt dataframe by subsetting tx_df columns based on row variant - "J3", "J10", "J11", "J13". Then, I converted the var_nt dataframe to a GRanges object (varnt_grange) using the makeGRangesFromDataFrame function.

            Now, I want to write a for loop to collapse the varnt_grange into a single vector.

            ...

            ANSWER

            Answered 2022-Feb-19 at 23:15

            On each iteration, you are inadvertently rewriting over the same object, repeatedly. Instead, you can iterate over the values in gene.list$entrez using lapply

            Source https://stackoverflow.com/questions/71189445

            QUESTION

            Excel::Writer::XSLX write embedded hyperlinks
            Asked 2022-Feb-16 at 21:54

            I have a text with hyperlink(s) as below.

            ...

            ANSWER

            Answered 2022-Feb-16 at 21:54

            Unfortunately that isn’t possible in Excel (and hence not in Excel::Writer::XLSX). It is only possible to have one hyperlink per cell.

            Source https://stackoverflow.com/questions/70524064

            QUESTION

            Dynamicly apply css changes on html code with js
            Asked 2022-Feb-10 at 08:52

            here's the situation

            I have a select element in my html code, with many option. One of these options is "Other". What I want is, when I select "Other", without refreshing the page, display an input element right under the select one with JS. The problem is that I have to refresh the page to see the change. Can you help me? :)

            There's my code :

            ...

            ANSWER

            Answered 2022-Feb-10 at 08:48

            You have to add an eventlistener.

            Source https://stackoverflow.com/questions/71062044

            QUESTION

            How to convert Entrez ids in a large list into gene symbols and replace entrez ids in list in R?
            Asked 2022-Feb-03 at 17:57

            I have a large list data with 300 names. For eg:

            ...

            ANSWER

            Answered 2022-Feb-03 at 17:57

            We may loop over the list and apply the bitr

            Source https://stackoverflow.com/questions/70975616

            QUESTION

            Displaying a div without it shifting the following elements
            Asked 2022-Jan-22 at 08:06

            Is there a css property that I can apply to the div containing the error message so that it can be displayed without it shifting the following elements as shown in this picture :

            This is my html code :

            ...

            ANSWER

            Answered 2022-Jan-22 at 08:06

            Use visibility property

            The visibility CSS property shows or hides an element without changing the layout of a document.

            Use line-height: 32px; to set the height of the message which indeed will set the gap between two inputs.

            You can either toggle the inline style

            Source https://stackoverflow.com/questions/70810078

            QUESTION

            How can i reorder a numpy array from high to low in another array without using in built functions
            Asked 2021-Dec-18 at 14:28

            i am having a bit of trouble here, plus i am new to using numpy. what i want to do is reorder the array T in V from high to low and changing the highest number to -1 everytime in the array T without using unbuilt functions i would truly appreciate any help, thank you.

            ...

            ANSWER

            Answered 2021-Dec-18 at 14:28

            For n == 5 I created both arrays as:

            Source https://stackoverflow.com/questions/70403230

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

            Vulnerabilities

            No vulnerabilities reported

            Install entrez

            You can download it from GitLab, GitHub.
            You can use entrez like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.

            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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            CLONE
          • HTTPS

            https://github.com/jordibc/entrez.git

          • CLI

            gh repo clone jordibc/entrez

          • sshUrl

            git@github.com:jordibc/entrez.git

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