machado | repository provides users with a framework to store | Genomics library

 by   lmb-embrapa Python Version: 0.5.0 License: GPL-3.0

kandi X-RAY | machado Summary

kandi X-RAY | machado Summary

machado is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. machado has no bugs, it has no vulnerabilities, it has build file available, it has a Strong Copyleft License and it has low support. You can install using 'pip install machado' or download it from GitHub, PyPI.

Machado is a Django application that contains tools to interact with a Chado database. It provides users with a framework to store, search and visualize biological data. Detailed documentation can be found in the docs directory (Read the docs).
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              machado has a low active ecosystem.
              It has 13 star(s) with 3 fork(s). There are 2 watchers for this library.
              OutlinedDot
              It had no major release in the last 12 months.
              There are 1 open issues and 19 have been closed. On average issues are closed in 5 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of machado is 0.5.0

            kandi-Quality Quality

              machado has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              machado 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

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

            Top functions reviewed by kandi - BETA

            kandi has reviewed machado and discovered the below as its top functions. This is intended to give you an instant insight into machado implemented functionality, and help decide if they suit your requirements.
            • Process an RNA - seq RNA - seq file
            • Return the number of lines in a file
            • Inserts a new organism
            • Retrieve an organism from a string
            • List all the coexpression group members
            • Returns a queryset of the queryset
            • List of orthologous features
            • Returns a queryset of all features in the feature property
            • Handle GET request
            • Retrieve data for a feature
            • Return the strand of an object
            • Return the end length of an object
            • Prepare a relationship
            • Prepare DOI objects
            • Return the start location of the object
            • List features
            • Returns a list of all subfeatures of the given object
            • Returns the DOI of the FeatureProperty
            • Prepare text for a feature
            • Return a list of individual features
            • Perform search
            • Returns context data
            • Returns a queryset queryset
            • Returns the feature annotation
            • Returns the display value
            • Patch all web services
            Get all kandi verified functions for this library.

            machado Key Features

            No Key Features are available at this moment for machado.

            machado Examples and Code Snippets

            No Code Snippets are available at this moment for machado.

            Community Discussions

            QUESTION

            How do I fix sorting issue in Cobol program?
            Asked 2021-Apr-13 at 07:49

            I have a program that is suppose to sort an input file (seq) and then output an RPT file.

            This program code should be correct, the problem should only be in the sorting of this program.

            PROBLEM: The program successfully sorts the data correctly, my problem is that I can not get the sort file to continue after being sorted to be formatted and do calculations.

            PLEASE: show in code and explain, this is my first time trying the sort a file.

            SEQ:

            ...

            ANSWER

            Answered 2021-Apr-13 at 07:49

            In the PERFOM UNTIL... loop, you are reading BASEBALL-FILE-OUT, instead of the sorted BASEBALL-FILE-SORTED.

            Source https://stackoverflow.com/questions/67067783

            QUESTION

            UPDATED: How do I fix Sort and Release in Cobol?
            Asked 2021-Apr-12 at 20:07

            I have a program that is suppose to sort an input file (seq) and then output an RPT file.

            This program code should be correct, the problem should only be in the sorting of this program.

            CURRENTLY: Program will not compile.

            SORT: The output records need to sort LEAGUE-S (major) in descending order. TEAM-S (intermediate) ascending order. NAME-S (minor) ascending order.

            PLEASE: show in code and explain, this is my first time trying the sort a file.

            SEQ:

            ...

            ANSWER

            Answered 2021-Apr-12 at 19:42

            ARE-THERE-MORE-RECORDS = 'NO' is still true from its use in the input procedure. At the beginning of the output procedure, insert MOVE 'YES' TO ARE-THERE-MORE-RECORDS. You also need to replace the READ BASEBALL-FILE-IN with RETURN SORT-FILE, add some fields to SORT-RECORD, and use those fields for the report.

            Why do you have BASEBALL-FILE-UNSORTED-IN? It doesn't have any of the fields you need to move to SORT-RECORD.

            If you want to use BASEBALL-FILE-UNSORTED-IN, then don't use an input procedure. Instead change the SORT statement from INPUT PROCEDURE 120-SORT-INPUT-PROCEDURE to USING BASEBALL-FILE-UNSORTED-IN. Do not OPEN or CLOSE the file. That will be done by the runtime. Remove the 120- and 130- paragraphs.

            Comment everything associated with BASEBALL-FILE-IN, except 01 BASEBALL-RECORD-IN and its data items. That effectively allows the BASEBALL-RECORD-IN data definition to be used as a replacement for SORT-RECORD. That reduces the number of changes that are needed.

            Source https://stackoverflow.com/questions/67064067

            QUESTION

            How do I fix sorting program?
            Asked 2021-Apr-12 at 17:57

            I have a program that is suppose to sort an input file (seq) and they output an RPT file.

            This program code should be correct, the problem should only be in the sorting of this program. Currently, it prints is weird chunks.

            SORT: The output records need to sort LEAGUE-S (major) in descending order. TEAM-S (intermediate) ascending order. NAME-S (minor) ascending order.

            SEQ:

            ...

            ANSWER

            Answered 2021-Apr-12 at 17:57

            SORT is not being used correctly. The report is being printed in 120-SORT-INPUT-PROCEDURE using the fields from BASEBALL-RECORD-IN. It should be printed in 130-SORT-OUTPUT-PROCEDURE using the fields from SORT-RECORD.

            Furthermore, no records are sorted because there is no RELEASE statement in the input procedure. To access records after the sort, a RETURN statement is used in the same manner as a READ statement for a sequential file.

            The input procedure should be used to move the data from selected records to the sort record, after which the record is released to sort.

            The output procedure may then used to produce a report from the sorted data by returning and printing each record until the there are no more sorted records.

            Source https://stackoverflow.com/questions/67061259

            QUESTION

            Accessing a Sub Array inside object through a Variable
            Asked 2021-Jan-06 at 15:53

            I am getting an Array from an API which looks like this:

            ...

            ANSWER

            Answered 2021-Jan-06 at 15:53

            What you're looking for is Square bracket notation which allows you to read a property based on a string.

            Source https://stackoverflow.com/questions/65598930

            QUESTION

            Anchor fragments in Angular 6
            Asked 2020-Mar-11 at 09:54

            I am trying to do something as simple as making anchor links that jump to a link on the same page. There is surprisingly only very limited documentation but I found following:

            Using anchor link #id in Angular 6

            @machado comment recommends following which seems like the correct approach:

            ...

            ANSWER

            Answered 2018-Oct-15 at 18:32

            You probably just need to modify your anchor to this removing the #.

            Source https://stackoverflow.com/questions/52822206

            QUESTION

            Python: Problems writing data to bootstrapTable
            Asked 2020-Feb-12 at 20:14

            I am trying to pass the data obtained through a select to a table, however I realize that there is a problem with "character encoding", I think.

            This example is the data output straight from the function that pulls data from the database:

            ...

            ANSWER

            Answered 2020-Feb-12 at 20:14

            Add |safe to disable automatic escaping.

            Source https://stackoverflow.com/questions/60195685

            QUESTION

            Chloropeth map in R not working out, I think the problem is in merging the data
            Asked 2020-Jan-29 at 00:19

            I'm trying to do a chloropeth map following this guide: https://www.r-graph-gallery.com/327-chloropleth-map-from-geojson-with-ggplot2.html

            I mixed a bit of the tutorial with this answer(Chloropleth map with geojson and ggplot2), since I wasn't getting the result I expected. The cities were being filled with the same color, and it seemed as R wasn't understanding the data as numeric, and filled every city that had at least 1 user with the default color. (tried using as.numeric, didnt work either)

            I downloaded "users by city" data from my website from Google Analytics using

            ...

            ANSWER

            Answered 2020-Jan-28 at 22:09

            It looks like you have a couple relatively large values, while most are small. This causes 'skewing' of your color scale in a way that looks less interesting. Instead of graphing number of users, consider mapping based on a quantile .

            Here is an implementation of grouping into quantiles using cut2() from Hmisc. In this case, values are cut into 5 groups.

            Source https://stackoverflow.com/questions/59954168

            QUESTION

            how to tokenize big text in sentences and words
            Asked 2019-Dec-26 at 19:53

            I'm working with nltk in language portuguese.

            That's is my text:

            ...

            ANSWER

            Answered 2019-Dec-13 at 04:26
            word_token  =  list(pytext1)  # if you want to have only word token from pytext1
            print(word_token[0:10]) # printing first 10 token
            
            #op
            ['Romance',',','Memórias','Póstumas','de','Brás','Cubas',',','1880','Memórias'] 
            
            #if you want sent_token of text using sent_tokenize, read textfile in raw form 
            raw_text = machado.raw('romance/marm05.txt')
            
            print(raw_text[0:100]) # printing first 100 character from sentence
            #op
            'Romance, Memórias Póstumas de Brás Cubas, 1880\n\nMemórias Póstumas de\nBrás Cubas\n\nTexto-fonte:\nObra C'
            
            sent_token = nltk.sent_tokenize(raw_text)
            print(sent_token[0:2]) # printing 2 sentence, which is tokenized from text
            
            ['Romance, Memórias Póstumas de Brás Cubas, 1880\n\nMemórias Póstumas de\nBrás 
            Cubas\n\nTexto-fonte:\nObra Completa, Machado de\nAssis,\nRio\nde Janeiro: Editora 
            Nova Aguilar, 1994.',
            'Publicado originalmente em\nfolhetins, a partir de março de 1880, na Revista Brasileira.']
            

            Source https://stackoverflow.com/questions/59309328

            QUESTION

            Select lines with a column value greather than another column value
            Asked 2019-Nov-16 at 17:35

            I'm trying to get the name of all authors that have more books than a specific author in my database.

            Schema: (LIVRO means BOOK)

            I have this query:

            ...

            ANSWER

            Answered 2019-Nov-16 at 17:35

            You could simply remove the COUNT() around the subquery, and move it within the suubquery itself:

            Source https://stackoverflow.com/questions/58893271

            QUESTION

            HTML has a margin bigger than body
            Asked 2019-Jun-02 at 14:48

            I'm creating my own personal site using bootstrap.

            I've using bootstrap4 with some modifications. However the html margin is bigger than body.
            I've already checked other questions and they say that

            or some other tag has a default margin and you need to zero that, however I'm using a reset.css and plus I tried to zero margin of a lot of elements and it didn't work.

            the reset css and the link to my web site: https://sitezinho--mateusmsouza.repl.co/

            ...

            ANSWER

            Answered 2019-Jun-01 at 18:59

            Fala Mateus, blz?


            Change margin: 0; to margin: 0 !important;

            This may fix it, but the correct way would be removing 'margin' from the class that is being applied to this element.


            Bets regards,

            Brhaka

            Source https://stackoverflow.com/questions/56409555

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

            Vulnerabilities

            No vulnerabilities reported

            Install machado

            Please refer to the complete documentation at Read the docs.

            Support

            Machado is run by volunteers and we are always looking for people interested in helping with code development, documentation writing, and bug report. If you wish to contribute, please create an issue.
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          • PyPI

            pip install machado

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            gh repo clone lmb-embrapa/machado

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