medusa | draft genome scaffolder that uses multiple reference genomes | Genomics library

 by   combogenomics Java Version: medusa-1.6 License: GPL-3.0

kandi X-RAY | medusa Summary

kandi X-RAY | medusa Summary

medusa is a Java library typically used in Artificial Intelligence, Genomics applications. medusa has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. However medusa build file is not available. You can download it from GitHub.

When medusa archive is unzipped the following files will be extracted:.

            kandi-support Support

              medusa has a low active ecosystem.
              It has 25 star(s) with 15 fork(s). There are 7 watchers for this library.
              It had no major release in the last 12 months.
              There are 6 open issues and 22 have been closed. On average issues are closed in 48 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of medusa is medusa-1.6

            kandi-Quality Quality

              medusa has 0 bugs and 0 code smells.

            kandi-Security Security

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

            kandi-License License

              medusa 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

              medusa releases are available to install and integrate.
              medusa 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.
              medusa saves you 1163 person hours of effort in developing the same functionality from scratch.
              It has 2625 lines of code, 169 functions and 17 files.
              It has high code complexity. Code complexity directly impacts maintainability of the code.

            Top functions reviewed by kandi - BETA

            kandi has reviewed medusa and discovered the below as its top functions. This is intended to give you an instant insight into medusa implemented functionality, and help decide if they suit your requirements.
            • The main entry point
            • Runs the scaffolds
            • Reads a MongoGraph from a file
            • Writes the given graph to the given file
            • Read node order
            • Get the out edges of a node
            • Compares this node to another
            • Given a node return a String representation of the original
            • Computes the cover
            • Return true if the edge is not a Vine
            • Reads the graph from information file
            • Adds an edge to this node
            • Get a list of all subChains
            • Create a hash code
            • Computes the cover between two groups
            • Compare two edges
            • Set the label info
            • Read the contig info of the contig
            • Remove cycles
            • Deduplicates all the edges in this graph
            • Computes a cover for this graph
            • Compares this edge to another Edge
            • Parses the specified file and returns a HashMap of IDs
            • Compute error errors
            • Reads the contig order from the specified file and returns a HashMap of the contiggers
            • Merge two components
            Get all kandi verified functions for this library.

            medusa Key Features

            No Key Features are available at this moment for medusa.

            medusa Examples and Code Snippets

            No Code Snippets are available at this moment for medusa.

            Community Discussions


            Why do I get this error when I'm trying to create models from database?
            Asked 2021-May-05 at 06:07

            I'm trying to create models from my Oracle database 10g using Entity Framework Core 5 dbcontext scaffold:



            Answered 2021-May-05 at 06:07

            The fine manual says minimum oracle 11.2 for that provider

            Upgrade your db or change provider



            Logback in a Java modular application not working
            Asked 2021-Apr-14 at 15:43

            I am just starting to master modular applications and I have a problem with the logback.

            Before modularity was introduced into the project, Logback successfully worked with the same settings.

            As soon as I start working with the LoggerContext and add the line requires ch.qos.logback.classic to the, the application crashes.

            Crash occurs in the line receiving the logger:



            Answered 2021-Apr-14 at 14:28


            How to read file into class in C++?
            Asked 2021-Apr-12 at 17:05

            I am reading File that contains



            Answered 2021-Apr-12 at 17:05

            This code reads your file and stores the data in the std::vector Info using stringstreams and other things to parse.



            Error when trying to retrieve from database
            Asked 2021-Feb-17 at 13:04

            I have generated three classes from XSD schema:



            Answered 2021-Feb-17 at 12:50

            We are missing the medusa initialization code, but you should do something like this:



            Extract distinct portions of long string with varying punctuation using RegEx
            Asked 2021-Jan-26 at 20:49

            I have a text file with many rows that generally follow the patterns shown below and I'd like to extract the segments numbered 1-4 in the image below. I cannot do it with Excel because the punctuation is not sufficiently consistent so I'd like to use RegEx.

            I am looking for 4 distinct RegEx expressions, corresponding to the 4 items.

            What I have so far:

            • (.+?(?=/)) gets me everything up to the / but I can't figure out how to split it in the Yellow and Cyan sections
            • (?<=\/\s)(.*) gets me everything after the / but includes the Mintmark portion

            Here is a good sample of the file contents:



            Answered 2021-Jan-26 at 20:49

            You could use a single pattern with 4 capturing groups.



            Format ansible output
            Asked 2021-Jan-05 at 15:19

            I have ansible role which checks the latest backups from my databases (cassandra and elasticsearch) so i have this output



            Answered 2021-Jan-05 at 15:19

            If the output of the ansible-playbook other/check_backup_status.yml -i hosts/mvd/prod/hosts.yml command goes to the standard output, I can redirect that output to awk in the next way:



            INNER JOIN SQL query includes duplicates
            Asked 2020-Nov-21 at 19:22

            I have an online store and am trying to display five similar products on the product page. There is a many-to-many relationship between products and tags which I'm trying to query (join table) using INNER JOIN. Here is the SQL query I have thus far:



            Answered 2020-Nov-21 at 18:30

            You can group by product and sort the results by the number of matched tags:



            d3.js multiple relationship visual / linkHorizontal() / tangled tree
            Asked 2020-Nov-05 at 03:58

            I am trying to mimic a visual that depicts multiple relationships by time period, like this (time period = generation):

            However, my efforts have not panned out thus far; I'm still getting blank output in the browser. Hard coded data and code in the snippet:



            Answered 2020-Oct-22 at 09:30

            I think a lot of what you did, specifically around data wrangling, was not necessary, especially since you called d3.hierarchy() and d3.cluster() afterwards. I've replaced this with d3.stratify (which deals with hierarchical data that is not yet in the right format).

            I've also replaced d3.cluster with d3.tree() because it was unclear to me why you'd want to use d3.cluster here. Your data has multiple parents, multiple roots and even floating nodes, and d3 is not meant to deal with that. My workaround has been to attach pseudonodes to every level, so as to make sure that there is only one node and that all nodes are at the right level at all times. To make sure the links were drawn correctly, I've written a custom getLinks function, that can deal with multiple parents.

            I've also written a custom link generator that draws the links somewhat in the way that you want them. d3 doesn't offer much of flexibility here, but you can use the source code for inspiration.


            I've changed the logic to be more focused on which "partners" got a child, so both links to the same child are on the same level - like in your picture. I've also drawn the nodes based on how many partners they have, and have given every link an offset so the lines are more distinct.

            I've sorted the nodes so that the real pro-creators are at the top (Zeus), which gives a more balanced and less crowded view.



            How to change property of element removed from array?
            Asked 2020-Jul-20 at 18:04

            this.statues.shift(); is isolating the correct element and removing it from the array. When this happens though, person.stoned needs to be false. Any pointers? Thank you.




            Answered 2020-Jul-18 at 22:14

            You need to save shifted object and set its property, like that:



            Find longest subsequence that contains letters with the same frequency in order
            Asked 2020-Jul-14 at 18:40

            This is a question from the 2019 Australian Informatics Olympiad Competition:

            After the success of your latest research project in mythical DNA, you have gained the attention of a most diabolical creature: Medusa. Medusa has snakes instead of hair. Each of her snakes’ DNA is represented by an uppercase string of letters. Each letter is one of S, N, A, K or E. Your extensive research shows that a snake’s venom level depends on its DNA. A snake has venom level x if its DNA:

            • has exactly 5x letters • begins with x copies of the letter S

            • then has x copies of the letter N

            • then has x copies of the letter A

            • then has x copies of the letter K

            • ends with x copies of the letter E.

            For example, a snake with venom level 1 has DNA SNAKE, while a snake that has venom level 3 has DNA SSSNNNAAAKKKEEE. If a snake’s DNA does not fit the format described above, it has a venom level of 0. Medusa would like your help making her snakes venomous, by deleting zero or more letters from their DNA. Given a snake’s DNA, can you work out the maximum venom level this snake could have?

            Is it possible using binary search to obtain an algorithm with complexity O(nlogn)?



            Answered 2020-Jul-14 at 14:05

            Yes you can use binary search to search for maximum venom level.

            initially: l=0 r=n

            when for some m=(l+r+1)/2 we can check in O(n) time if we can obtain such venom level m, just by taking first m letters S then next m letters N and so on. If there's not enough letters we update our search interval to r=m-1 otherwise l=m

            Example: suppose input is SNAKESSSNNAAKKE

            1. Binary search initial values: l=0 r=15
            2. l=0 r=15 m = (l+r+1)/2 = 8
            3. we cant get venom value of 8 so r=m-1 = 7
            4. l=0 r=7 m = (l+r+1)/2 = 4
            5. we cant get venom value of 4 so r=m-1 = 3
            6. l=0 r=3 m = (l+r+1)/2 = 2
            7. we can get venom value of 2 so l=m = 2
            8. l=2 r=3 m = (l+r+1)/2 = 3
            9. we cant get venom value of 3 so r=m-1 = 2
            10. now since l==r we terminate binary search and conclude that answer is 2


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


            No vulnerabilities reported

            Install medusa

            You can download it from GitHub.
            You can use medusa like any standard Java library. Please include the the jar files in your classpath. You can also use any IDE and you can run and debug the medusa component as you would do with any other Java program. Best practice is to use a build tool that supports dependency management such as Maven or Gradle. For Maven installation, please refer For Gradle installation, please refer .


            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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