SnpEff

by pcingola Java Version: Current License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(3)Vulnerabilities Install Support

kandi X-RAY | SnpEff Summary

SnpEff is a Java library. SnpEff has no bugs, it has no vulnerabilities, it has build file available and it has low support. However SnpEff has a Non-SPDX License. You can download it from GitHub.

SnpEff

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Quality

Security

License

Reuse

Support

SnpEff has a low active ecosystem.

It has 173 star(s) with 71 fork(s). There are 21 watchers for this library.

It had no major release in the last 6 months.

There are 89 open issues and 313 have been closed. On average issues are closed in 23 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of SnpEff is current.

Quality

SnpEff has no bugs reported.

Security

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

License

SnpEff has a Non-SPDX License.

Non-SPDX licenses can be open source with a non SPDX compliant license, or non open source licenses, and you need to review them closely before use.

Reuse

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

Build file is available. You can build the component from source.

Top functions reviewed by kandi - BETA

kandi has reviewed SnpEff and discovered the below as its top functions. This is intended to give you an instant insight into SnpEff implemented functionality, and help decide if they suit your requirements.

Set all fields from a variantEffect
Return the SequenceOntology for this sequence
Calculates the genomic position of the sequence
Returns a string representation of this SNPs
Parses the command line arguments
Displays usage information
Reads a file and returns it as a string
Compares two variant effects
Convert TranscriptSupportLevel to TSL support
Reads the next rule
Calculates the effect
Get the homet table
Calculates alignment
Parse the command database arguments
Generate evenly spaced paints
Reads the next motif
Creates a new sequence by combining two sequences
Performs sanity checks
Returns a string representation of the results
Attempts to guess the type of VCF information
Calculate entities
Read an OBO file
Runs the analysis
Initialize the cache
Parse an XML element
Get a subfield by its name

Get all kandi verified functions for this library.

SnpEff Key Features

No Key Features are available at this moment for SnpEff.

SnpEff Examples and Code Snippets

No Code Snippets are available at this moment for SnpEff.

Community Discussions

Trending Discussions on SnpEff

Snakemake on cluster error: 'Wildcards' object has no attribute 'output'

Adjusting labels on bar chart ggplot2, non-dependent on data value

Using bash functions in snakemake

QUESTION

Snakemake on cluster error: 'Wildcards' object has no attribute 'output'

Asked 2022-Jan-11 at 14:29

I'm running into an error of 'Wildcards' object has no attribute 'output', similar to this earlier question 'Wildcards' object has no attribute 'output', when I submit Snakemake to my cluster. I'm wondering if you have any suggestions for how to make this compatible with the cluster?

While my rule annotate_snps works when I test it locally, I get the following error on the cluster:

...

ANSWER

Answered 2022-Jan-11 at 14:29

The raw rule definition appears to be consistent except for the multiple calls to the contents of config, e.g. config[snpeff].

One thing to check is if the config definition on the single machine and on the cluster is the same, if it's not there might be some content that is confusing snakemake, e.g. if somehow config[snpeff] == "wildcards.output" (or something similar).

Source https://stackoverflow.com/questions/70615842

QUESTION

Adjusting labels on bar chart ggplot2, non-dependent on data value

Asked 2020-Mar-30 at 20:56

I added labels to my bar chart using hjust, but for some reason they are farther away for the bars that have higher values. Ideally I want them all to be rather close to each bar.

...

ANSWER

Answered 2020-Mar-30 at 20:56

hjust varies between 0 and 1, generally, with 0.5 being center justified. I'd recommend setting hjust = 0 and then using the nudge adjusters to tweak the amount in data coordinates. For example:

Source https://stackoverflow.com/questions/60939041

QUESTION

Using bash functions in snakemake

Asked 2020-Feb-14 at 15:17

I am trying to download some files with snakemake. The files (http://snpeff.sourceforge.net/SnpSift.html#dbNSFP) I would like to download are on a google site/drive and my usual wget approach does not work. I found a bash function that does the job (https://www.zachpfeffer.com/single-post/wget-a-Google-Drive-file):

...

ANSWER

Answered 2020-Feb-08 at 18:33

You would want to use raw string literal so that snakemake doesn't escape special characters, such as backslash in sed command. For example (notice r in front of shell command):

Source https://stackoverflow.com/questions/60127866

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

Vulnerabilities

No vulnerabilities reported

Install SnpEff

You can download it from GitHub.
You can use SnpEff 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 SnpEff 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 maven.apache.org. For Gradle installation, please refer gradle.org .

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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