Prodigal | Prodigal Gene Prediction Software | Genomics library

by hyattpd C Version: v2.6.3 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(10)Vulnerabilities Install Support

kandi X-RAY | Prodigal Summary

Prodigal is a C library typically used in Artificial Intelligence, Genomics applications. Prodigal has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Fast, reliable protein-coding gene prediction for prokaryotic genomes.

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Quality

Security

License

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Support

Prodigal has a low active ecosystem.

It has 354 star(s) with 76 fork(s). There are 24 watchers for this library.

It had no major release in the last 12 months.

There are 29 open issues and 58 have been closed. On average issues are closed in 333 days. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of Prodigal is v2.6.3

Quality

Prodigal has no bugs reported.

Security

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

License

Prodigal 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.

Reuse

Prodigal releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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Prodigal Key Features

No Key Features are available at this moment for Prodigal.

Prodigal Examples and Code Snippets

No Code Snippets are available at this moment for Prodigal.

Community Discussions

Trending Discussions on Prodigal

How do i create env from .yml file in conda in windows?

How to extract all smart contracts on the Ethereum blockchain?

Snakemake "Missing files after X seconds" error

Missing input files for rule all in snakemake

JavaScript: Search function, remove unordered list elements with search bar input

Iterating through a series of GenBank genes and appending each gene's features to a list returns only the last gene

How to get files generated by docker run to host

Extract substring with sed/awk/grep from .gff file

split extra-delimited column from prokka gff table with varying number of entries into new columns with NAs (splitstackshape / R)

awk selecting multiple columns starting with specific strings and print to the last field

QUESTION

How do i create env from .yml file in conda in windows?

Asked 2020-Aug-03 at 00:49

I have just started using miniconda on windows and was creating an environment through a .yml file but got this error.

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ANSWER

Answered 2020-Aug-03 at 00:49

There are a couple of issues. First, going across platforms (linux-64 to win-64) is not directly supported. There are other answers that address this. Second, and more prohibitive, is that Bioconda does not support Windows and some of the packages (e.g., hmmer) are specifically from there.

Alternatives could be either building up the dependencies in Conda env, plus a compiler meta-package (compiler-cxx, make), then installing non-Windows software from source (e.g., see HMMER documentation); or running Conda under WSL.

Source https://stackoverflow.com/questions/63214608

QUESTION

How to extract all smart contracts on the Ethereum blockchain?

Asked 2020-Jun-20 at 10:13

My goal is to find greedy, prodigal, and suicidal smart contracts on the Ethereum blockchain. Is there any trick that by using that I could extract all smart contracts on Ethereum blockchain?

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ANSWER

Answered 2020-Jun-20 at 10:13

Get an Ethereum node
Walk all mined Ethereum blocks from genesis block 1 - to latest you can e.g. use Web3.py or Web3.js to interact with your node API
Check all transactions in a block - use web3.eth.getTransactionFromBlock
If the transaction is a contract deployment transaction you have your smart contract

Source https://stackoverflow.com/questions/62451202

QUESTION

Snakemake "Missing files after X seconds" error

Asked 2019-Dec-05 at 11:28

I am getting the following error every time I try to run my snakemake script:

...

ANSWER

Answered 2019-Dec-05 at 11:28

In rule pear I think you want to use the shell directive instead of run. With run you execute python code which in this case does nothing as you simply "execute" a string so you get no error and no file produced.

Source https://stackoverflow.com/questions/59191168

QUESTION

Missing input files for rule all in snakemake

Asked 2019-Nov-28 at 13:25

I am trying to construct a snakemake pipeline for biosynthetic gene cluter detection but am struggling with the error:

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ANSWER

Answered 2019-Nov-28 at 12:38

(Since I can't comment yet ...) You might have a problem with your relative paths, and we cannot see where your files actually are found.

A way to debug this is to use config["path_to_files"] to create absolute paths in input: That would give you better error message on where Snakemake expects the files - input/output files are relative to the working directory.

Source https://stackoverflow.com/questions/59085429

QUESTION

JavaScript: Search function, remove unordered list elements with search bar input

Asked 2019-Aug-22 at 12:14

I have a div.header with a div. search where my input tag exists with my call function. I also have div.content with all the elements to search for. They are located in different div tags, but the call function for my JavaScript is only in the input tag. Problem is when i type in the input tag my console tells me this:

(21) Champions.htm:564 Uncaught TypeError: li.getElementsByClassName is not a function at searchfunction (Champions.htm:564) at HTMLInputElement.onkeyup (Champions.htm:39)

The solution I'm looking for is how I make my input tag remove search elements when I type in a specific champion name. Example:

Typing in A into the input tag should remove all the elements with h3 tags that don't match the search criteria.

Note: My h3 tags are filled in with specific names. And these names are what the searchfunction() should be looking for and removing from the page if they don't match the search criteria.

I'm not much of a JavaScript fan, so most of my tries have been in vain.

...

ANSWER

Answered 2019-Aug-22 at 08:41

li is an array as getElementsByTagName will return array. You have to either iterate through it or use index in order to use getElementsByClassName

Source https://stackoverflow.com/questions/57604954

QUESTION

Iterating through a series of GenBank genes and appending each gene's features to a list returns only the last gene

Asked 2019-Mar-13 at 19:35

I'm having a problem with my code. I'm trying to iterate through the genbank file's list of genes using BioPython. Here's what it looks like:

...

ANSWER

Answered 2019-Mar-12 at 18:24

You are never creating any instances of the genBank class. Each loop iteration is changing class-level attributes of the genBank class, and you are adding the same object to the list each time. Each pass through the loop overwrites the values in the previous pass.

For the first line in your inner loop, add parenthesis to call the type and create an instance of genBank. It will instead be genBankEntry = genBank(). This creates a new distinct object for each loop pass.

Source https://stackoverflow.com/questions/55128143

QUESTION

How to get files generated by docker run to host

Asked 2018-Oct-29 at 09:03

I have run docker run to generate a file

...

ANSWER

Answered 2018-Oct-29 at 09:03

I assume your dest path does not exist. Docker cp doc stats that in that case :

Source https://stackoverflow.com/questions/53041595

QUESTION

Extract substring with sed/awk/grep from .gff file

Asked 2018-Jul-16 at 14:55

I have a file containing multiple lines like this:

...

ANSWER

Answered 2018-Jul-16 at 14:42

You may use grep -oE:

Source https://stackoverflow.com/questions/51363954

QUESTION

split extra-delimited column from prokka gff table with varying number of entries into new columns with NAs (splitstackshape / R)

Asked 2018-Jun-05 at 13:29

I have a file including tab separated and semicolon separated data (a prokka annotation file in .gff format). Unfortunately, the semicolon separated part is not consistent in the number of entries.

Fortunately, though, the leading part after the semicolon (e.g. ID= or gene=) is consistent. I would like to prepare this data as input for R (or within R) without different column numbers or empty fields. These are the first lines from the prokka file, with some columns removed:

...

ANSWER

Answered 2018-Jun-05 at 13:21

An option using tidyverse and splitstackshape can be achieved. First read the file data using say read.table (with argument sep="\t"). Then split the column V5 using splitstackshape::splitstackshape in to different columns. Now data is ready to be changed to long format and processed.

Source https://stackoverflow.com/questions/50686019

QUESTION

awk selecting multiple columns starting with specific strings and print to the last field

Asked 2018-Mar-19 at 17:51

I'm looking for a way to pimp this command, which checks for a column starting with a certain string ("product=") and prints the respective column (and many following and the second and the third, based on ";" as delimiter).

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ANSWER

Answered 2018-Mar-19 at 17:51

Considering that your actual Input_file is same as shown sample if yes then could you please try following awk and let me know if this helps you.

Source https://stackoverflow.com/questions/49367773

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

Vulnerabilities

No vulnerabilities reported

Install Prodigal

Prodigal consists of a single binary, which is provided for Linux, Mac OS X, and Windows with each official release. You can also install from source (you will need Cygwin or MinGW on Windows) as follows:. For more detail, see Installing Prodigal.

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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