tag | Genome annotation data analysis and management | Genomics library

 by   standage Python Version: 0.5.1 License: BSD-3-Clause

kandi X-RAY | tag Summary

kandi X-RAY | tag Summary

tag is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. tag has no bugs, it has no vulnerabilities, it has build file available, it has a Permissive License and it has low support. You can download it from GitHub.

Computational biology is 90% text formatting and ID cross-referencing! -- discouraged graduate students everywhere. tag is a free open-source software package for analyzing genome annotation data. To install the most recent stable release execute pip install tag from your terminal. Full installation instructions and project documentation are available at
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            kandi-support Support

              tag has a low active ecosystem.
              It has 8 star(s) with 0 fork(s). There are 2 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 5 open issues and 25 have been closed. On average issues are closed in 110 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of tag is 0.5.1

            kandi-Quality Quality

              tag has no bugs reported.

            kandi-Security Security

              tag has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

            kandi-License License

              tag is licensed under the BSD-3-Clause License. This license is Permissive.
              Permissive licenses have the least restrictions, and you can use them in most projects.

            kandi-Reuse Reuse

              tag releases are available to install and integrate.
              Build file is available. You can build the component from source.
              Installation instructions are not available. Examples and code snippets are available.

            Top functions reviewed by kandi - BETA

            kandi has reviewed tag and discovered the below as its top functions. This is intended to give you an instant insight into tag implemented functionality, and help decide if they suit your requirements.
            • Return a dict containing the command - line arguments
            • Open filehandle
            • Get the project root directory
            • Extract version information from the VCS
            • Create a ConfigParser from a root directory
            • Merges overlapping ranges
            • Returns the overlap between two intervals
            • Returns True if this interval overlaps with another
            • Create the versioneer config file
            • Install versioneer
            • Generator yielding features from an entry stream
            • Filter an entry stream
            • Returns the span of the interval set
            • Get the extent for a seqid
            • Consume a GFF3 tag
            • Returns True if this node is a parent
            • Collapse a locus stream
            • Scans the setup py and returns a boolean indicating whether it is missing
            • Evaluate a locus stream
            • Yield directives from an entry stream
            • Return NCBI GeneID
            • Sequence of locus
            • Convert a PEP3 tag to protein features
            • Return a string representation of the object
            • Get keywords from a git version file
            • Extract the version information
            • Extract sequences from an entry stream
            Get all kandi verified functions for this library.

            tag Key Features

            No Key Features are available at this moment for tag.

            tag Examples and Code Snippets

            tag: Toolkit for Annotating Genomes
            Pythondot img1Lines of Code : 6dot img1License : Permissive (BSD-3-Clause)
            copy iconCopy
            # Compute number of exons per gene
            import tag
            reader = tag.GFF3Reader(infilename='/data/genomes/mybug.gff3.gz')
            for gene in tag.select.features(reader, type='gene'):
                exons = [feat for feat in gene if feat.type == exon]
                print('num exons:', len  

            Community Discussions

            QUESTION

            Elastic beanstalk deploy fails when deploying more than 4 containers using docker compose
            Asked 2021-Jun-16 at 03:01

            I am having this weird issue with elastic beanstalk. I am using docker compose to run multiple docker containers on same elastic beanstalk instance.

            if I run 4 docker containers everything works fine. but if i make it 5, deploy fails with error Instance deployment failed to download the Docker image. The deployment failed. and if I check eb-engine.log. it retries to docker pull command and fails with error.

            this is really weird error. bcs all docker images are valid and correctly tagged. it just the number of services that I am adding in docker compose file. if number is greater than 4, deploy fails

            my question is, is there any limit of docker services that can be run using docker compose ? or is there any timeout in elastic beanstalk to pull images?

            ...

            ANSWER

            Answered 2021-Jun-16 at 03:01

            Based on the comments.

            The issue was that t2.micro instance was used. The instance has only 1 vCPu and 1GB of ram. This was not enough to run 5 docker containers. Changing instance type to t2.large with 8GB ram and 2 vCPUs solved the problem.

            docker-compose allows to specify cpu and memory limits. Maybe you can set them up to keep your containers resource requirements in check.

            Source https://stackoverflow.com/questions/67977894

            QUESTION

            How to Config Javascript ' script in Django?
            Asked 2021-Jun-16 at 02:47

            I built an app using Django 3.2.3., but when I try to settup my javascript code for the HTML, it doesn't work. I have read this post Django Static Files Development and follow the instructions, but it doesn't resolve my issue.

            Also I couldn't find TEMPLATE_CONTEXT_PROCESSORS, according to this post no TEMPLATE_CONTEXT_PROCESSORS in django, from 1.7 Django and later, TEMPLATE_CONTEXT_PROCESSORS is the same as TEMPLATE to config django.core.context_processors.static but when I paste that code, turns in error saying django.core.context_processors.static doesn't exist.

            I don't have idea why my javascript' script isn't working.

            The configurations are the followings

            Settings.py

            ...

            ANSWER

            Answered 2021-Jun-15 at 18:56

            Run ‘python manage.py collectstatic’ and try again.

            The way you handle static wrong, remove the static dirs in your INSTALLED_APPS out of STATIC_DIRS and set a STATIC_ROOT then collectstatic again.

            Add the following as django documentation to your urls.py

            Source https://stackoverflow.com/questions/67990678

            QUESTION

            Invalid Character when Selecting classname - Python Webscraping
            Asked 2021-Jun-16 at 01:11

            I am beginning to learn the basics of webscraping with Python, but I am having a little trouble with my code. I am trying to scrape the weather from the front page of 'yahoo.com':

            ...

            ANSWER

            Answered 2021-Jun-16 at 01:11

            The problem is that your CSS selectors include parentheses () and dollar signs $. These symbols already have a special meaning. See:

            You can escape these characters using a backslash \.

            Source https://stackoverflow.com/questions/67994434

            QUESTION

            Search Filter in RecyclerView not showing anything
            Asked 2021-Jun-15 at 21:08

            My app consists in letting you add lists in which you can keep your notes. Therefore, I have this NotesListActivity where I can add and keep my Lists. I wanted to filter this lists following the https://www.youtube.com/watch?v=CTvzoVtKoJ8 tutorial and then I tried to adapt it to my code like below. Could you please tell me what is the problem here, cause I don't even get an error, I just not get any title of list as result. So, this is what I have in my RecyclerAdapter:

            ...

            ANSWER

            Answered 2021-Jun-13 at 20:18

            The problem is that you are using an empty notesListAll list for filtering results; you need to populate it with the list of notes in the constructor

            Source https://stackoverflow.com/questions/67957686

            QUESTION

            How to get rid of vertical hover gaps in a wrapped anchor tag?
            Asked 2021-Jun-15 at 20:57

            When I hover over the anchor tag, it flickers. It's because there are vertical gaps between the lines of the wrapped anchor tag. Moreover, if I happen to click between the lines, the link doesn't activate. I would like to get rid of this flickering and vertical hover gaps that cause it. The rest of the layout including apparent line height and button position (on the same line as the last word of the anchor tag) should stay the same.

            I was thinking about this for a couple of days with no luck. The best alternative I have is using inline-block on the anchor tag, but that clears the button to the next line, which wastes too much space.

            ...

            ANSWER

            Answered 2021-Jun-15 at 20:57

            QUESTION

            How could I mock a connection in apollo with graphQL to test in jest?
            Asked 2021-Jun-15 at 20:47

            I'm trying to somehow test a hooked file that uses an Apollo client connection entry and GraphQL:

            See the error:

            ...

            ANSWER

            Answered 2021-Jun-15 at 20:47

            I finally found the solution to the problem:

            Source https://stackoverflow.com/questions/67944184

            QUESTION

            copy a string form a line and paste at the end in another line for a huge file based on pattern
            Asked 2021-Jun-15 at 20:47

            I have the below requirement . i am trying to run the condition in loop and its taking more time. is there a one time command anything which will not take more time to process a 70 MB file.

            Requirement: if @pRECTYPE="SBSB" line contains @pSBEL_MCTR_RSN="XXX" tag then we need to copy and append that to next @pRECTYPE="SBEL record at the end of the line

            File :note : in file there will be no blank lines. I have given enter to avoid line continuation

            @pRUKE=dfgt@pRECTYPE="SMDR", @pCONFIG="Y" XXXXXXX

            @pRUKE=dfgt@pRECTYPE="SBSB", @pGWID="1234", @pSBEL_MCTR_RSN="KX28", @pSBSB_9000_COLL=""

            @pRUKE=dfgt@pRECTYPE="KBSG", @pKBSG_UPDATE_CD="IN", XXXXXXXXXXX

            @pRUKE=dfgt@pRECTYPE="SBEL", @pSBEL_EFF_DT="01/01/2017", @pCSPI_ID="JKOX0001", @pSBEL_FI="A"

            @pRUKE=dfgt@pRECTYPE="SBEK", @pSBEK_UPDATE_CD="IN",XXXXXXXXXXXXXXXXXXX

            @pRUKE=dfgt@pRECTYPE="DBCS", @pDBCS_UPDATE_CD="IN",XXXXXXXXXXXXXXXXXXXXXXXXXX

            @pRUKE=dfgt@pRECTYPE="MEME", @pMEME_REL="18", @pMEEL_MCTR_RSN="KX28"

            @pRUKE=dfgt@pRECTYPE="ATT0", @pATT0_UPDATE_CD="AP",XXXXXXXXX

            @pRUKE=dfgt@pRECTYPE="SBSB", @pGWID="1234", @pSBEL_MCTR_RSN="KX28", @pSBSB_9000_COLL=""

            @pRUKE=dfgt@pRECTYPE="KBSG", @pKBSG_UPDATE_CD="IN", XXXXXXXXXXX

            example :

            Before : @pRUKE=dfgt@pRECTYPE="SMDR", @pCONFIG="Y" XXXXXXX

            @pRUKE=dfgt@pRECTYPE="SBSB", @pGWID="1234", @pSBEL_MCTR_RSN="KX28", @pSBSB_9000_COLL=""

            @pRUKE=dfgt@pRECTYPE="KBSG", @pKBSG_UPDATE_CD="IN", XXXXXXXXXXX

            @pRUKE=dfgt@pRECTYPE="SBEL", @pSBEL_EFF_DT="01/01/2017", @pCSPI_ID="JKOX0001", @pSBEL_FI="A"

            After:

            @pRUKE=dfgt@pRECTYPE="SMDR", @pCONFIG="Y" XXXXXXX

            @pRUKE=dfgt@pRECTYPE="SBSB", @pGWID="1234", @pSBEL_MCTR_RSN="KX28", @pSBSB_9000_COLL=""

            @pRUKE=dfgt@pRECTYPE="KBSG", @pKBSG_UPDATE_CD="IN", XXXXXXXXXXX

            @pRUKE=dfgt@pRECTYPE="SBEL", @pSBEL_EFF_DT="01/01/2017", @pCSPI_ID="JKOX0001", @pSBEL_FI="A", @pSBEL_MCTR_RSN="KX28"

            if after SBSB, if there is no SBEL, then that SBSB can be ignored.

            what i did is egrep -n "pRECTYPE="SBSB"|pRECTYPE="SBEL"" filename | sed '$!N;/pRECTYPE="SBEL"/P;D' | awk -F: '{print $1}' | awk 'NR%2{printf "%s,",$0;next;}1' > 4.txt;

            by this i will get the line number eg: 2,4 17,19

            line 9 12 14 will be ignored

            while read line do

            ...

            ANSWER

            Answered 2021-Jun-15 at 20:47

            For performance, you need to really limit how many external tools you invoke inside a loop in a shell script.

            This requires GNU awk:

            Source https://stackoverflow.com/questions/67992675

            QUESTION

            Nested JSON Converting Rows
            Asked 2021-Jun-15 at 18:59

            Here are the 3 rows of my sample json.

            ...

            ANSWER

            Answered 2021-Jun-11 at 04:35

            I think you need to take the actual raw strings of JSON data and convert them into a list of objects (dicts).

            Source https://stackoverflow.com/questions/67930977

            QUESTION

            I want to loop through my array and calculate my values-JavaScript
            Asked 2021-Jun-15 at 18:46

            I want to able to loop my arrays and calculate the total price and display it in the console. this is suppose to be a cart application. I assign all the anchor tags to cart variable that loops through the anchors tag and assign the the tags to the values in my beverages array to be able to display it but i cant display the total amount of all the prices.

            html

            ...

            ANSWER

            Answered 2021-Jun-15 at 18:46

            Instead of writing too much and looping .... See this , it might help you build what you are willing too

            HTML

            Source https://stackoverflow.com/questions/67990964

            QUESTION

            Shorthand object initializer syntax for matching property name
            Asked 2021-Jun-15 at 18:36

            Sometimes I find myself needing to initialize an object with a property that matches the property of another object. When the property name is the same, I want to be able to use shorthand syntax.

            (For the purposes of the examples in this question, I'll just keep the additional properties to a tag: 1 property, and I'll reuse message in subsequent examples as the input/source of the information. I also indicate an extra unwanted property of message because I'm cherry-picking properties and do not intend to just use Object.assign to assign all the properties of message to the result.)

            ...

            ANSWER

            Answered 2021-Jun-15 at 16:26

            The best I have so far is { person: message.person, tag: 1 }.

            Is there shorthand initializer syntax to achieve this?

            No, this is still they way to go.

            hoping that a property name would magically be inferred from person

            Source https://stackoverflow.com/questions/67989808

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

            Vulnerabilities

            No vulnerabilities reported

            Install tag

            You can download it from GitHub.
            You can use tag 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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