sequencework | mainly python , for analyses | Genomics library

 by   fomightez Python Version: Current License: No License

kandi X-RAY | sequencework Summary

kandi X-RAY | sequencework Summary

sequencework is a Python library typically used in Healthcare, Pharma, Life Sciences, Artificial Intelligence, Genomics applications. sequencework has no bugs, it has no vulnerabilities and it has low support. However sequencework build file is not available. You can download it from GitHub.

Mainly python scripts related to nucleic or protein sequence work. I sorely need to put an index here with links to better guide to the appropriate folders. = TO DO (For now look at the title of the folders to try and discern if it is something of interest.). Descriptions of the scripts are found within README.md files in the sub folders.
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            kandi-support Support

              sequencework has a low active ecosystem.
              It has 18 star(s) with 5 fork(s). There are 3 watchers for this library.
              OutlinedDot
              It had no major release in the last 6 months.
              There are 1 open issues and 1 have been closed. On average issues are closed in 8 days. There are no pull requests.
              It has a neutral sentiment in the developer community.
              The latest version of sequencework is current.

            kandi-Quality Quality

              sequencework has no bugs reported.

            kandi-Security Security

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

            kandi-License License

              sequencework does not have a standard license declared.
              Check the repository for any license declaration and review the terms closely.
              OutlinedDot
              Without a license, all rights are reserved, and you cannot use the library in your applications.

            kandi-Reuse Reuse

              sequencework releases are not available. You will need to build from source code and install.
              sequencework 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.

            Top functions reviewed by kandi - BETA

            kandi has reviewed sequencework and discovered the below as its top functions. This is intended to give you an instant insight into sequencework implemented functionality, and help decide if they suit your requirements.
            • Plots a 5 - prime end plot
            • Extract scores from a bedgraph file
            • Generate an output file name for a sequence
            • Get the id of a sequence element
            • Convert MSA to residue numbers
            • Build a list of intervals from a list of lists
            • Determine if a match block ends in a match block
            • Calculate the equivalence between two sequences
            • Combine residue based on alignment
            • Extract regions from the alignment
            • Fix lsu_rRNA_annotation in gff_result
            • Checks if the given pattern matches the given pattern
            • Calculate the cons for each protein in the alignment
            • Calculates the coordination number for each nucleotide in the alignment
            • Computes the score of sequences in the alignment
            • Convert bendit results to Pandas DataFrames
            • Plot the sites in the genome
            • Calculate the score of sequences in the alignment
            • Tries to find motifs in the given sequence file
            • Plots two nucleotides in proximity difference between two nucleotides
            • Plots the nucleotide difference between two nucleotide sequences
            • Create a dict of motifs from a text file
            • Score differences between two sequences
            • Check if the chromosome is rearranged
            • Reverse the complement of the given alignment
            • Extract a subsequence from a FASTA file
            Get all kandi verified functions for this library.

            sequencework Key Features

            No Key Features are available at this moment for sequencework.

            sequencework Examples and Code Snippets

            No Code Snippets are available at this moment for sequencework.

            Community Discussions

            QUESTION

            Why have a supervision tree instead just one centralised supervisor?
            Asked 2020-Aug-13 at 05:12

            I'm learning Elixir and Erlang/OTP and would like to understand the significance of having a supervision tree in building highly available system.

            I can see the importance of a supervisor in managing the lifetime of worker processes. But, I still would like to know why do some applications have the need to organise supervisors in the form of hierarchies, instead of just having a single supervisor to manage all the workers? Are there any practical benefits of having such structures that I naively overlooked?

            Borrowing an example from the Programming Elixir book, in which scenario do we prefer the first structure over the second structure?

            ...

            ANSWER

            Answered 2020-Aug-13 at 05:12

            What you probably overlook is the famous “let it crash” philosophy, which makes process crashes and restarts the first-class citizen in OTP. We don’t treat process crashes as failures, but rather as an opportunity to redo it properly without the necessity to manually handle errors.

            The main reason is to allow more grained control on what should have been restarted on failure. For that, we have strategies. Or, as @Andree restated it in comments:

            by organizing supervisions in hierarchies, we allow finer-grained control over how the system should respond should a subset of the system fails

            Imagine the application that has a process responsible for a remote connection, and a bunch of processes, all using this resource. When the connection process crashes, it’s, in any case, being restarted by its supervisor but its pid changes. Meaning all the process that relied on this pid should have been restarted as well. With :rest_for_one strategy it’s easy out of the box.

            Another approach to this particular example would be to manage a connection in a process, supervised in another part of the tree, and upon connection issues manually crash the supervisor of pools using this connection to reinitialize all of them.

            Even more, we might want to manually crash the process handling this connection to reinitialize it, instead of writing defensive code like if no_conn, do: reload_config_and_restart_connection we just let it crash and get reinitialized by the supervision tree with new proper config.

            Last but not least, if the supervisor does not trap exits, it would crash as well, propagating it up. That way we might reinitialize the whole branch of supervision tree without writing a line of code.

            Source https://stackoverflow.com/questions/63387392

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

            Vulnerabilities

            No vulnerabilities reported

            Install sequencework

            You can download it from GitHub.
            You can use sequencework 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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          • CLI

            gh repo clone fomightez/sequencework

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            git@github.com:fomightez/sequencework.git

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