sequencework | mainly python , for analyses | Genomics library
kandi X-RAY | sequencework Summary
kandi X-RAY | sequencework Summary
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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- 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
sequencework Key Features
sequencework Examples and Code Snippets
Community Discussions
Trending Discussions on sequencework
QUESTION
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 05:12What 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.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install sequencework
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.
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