RepeatMasker | screens DNA sequences for interspersed repeats | Database library

by rmhubley Perl Version: Current License: Non-SPDX

X-Ray Key Features Code Snippets Community Discussions(5)Vulnerabilities Install Support

kandi X-RAY | RepeatMasker Summary

RepeatMasker is a Perl library typically used in Database applications. RepeatMasker has no bugs, it has no vulnerabilities and it has low support. However RepeatMasker has a Non-SPDX License. You can download it from GitHub.

Updates of the RepeatMasker program are distributed with a copy of the Dfam database ( www.dfam.org ). Dfam is a small but growing "open" databases of Transposable Element seed alignments, profile Hidden Markov Models and consensus sequences. RepeatMasker is also compatible with the RepBase database managed by the Genetic Information Research Institute and requires a license to use. Up until 2019 we maintained the "Repbase RepeatMasker Edition" libraries as co-editor of RepBase Update. For newer versions of RepBase users will need to use the sequences in FASTA format with RepeatMasker's "-lib" option. RepeatMasker "open-4.0" and later versions are distributed under the Open Source License. Please read LICENSE file for more information.

Support

Quality

Security

License

Reuse

Support

RepeatMasker has a low active ecosystem.

It has 169 star(s) with 43 fork(s). There are 6 watchers for this library.

It had no major release in the last 6 months.

There are 66 open issues and 131 have been closed. On average issues are closed in 96 days. There are 2 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of RepeatMasker is current.

Quality

RepeatMasker has no bugs reported.

Security

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

License

RepeatMasker 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

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

Installation instructions are not available. Examples and code snippets are available.

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RepeatMasker Key Features

No Key Features are available at this moment for RepeatMasker.

RepeatMasker Examples and Code Snippets

No Code Snippets are available at this moment for RepeatMasker.

Community Discussions

Trending Discussions on RepeatMasker

Plotly-igraph plotting a tree with variable number of children nodes?

How to import .OUT file into R?

Can't locate Text/Soundex.pm in @INC

Perl Module still not found after install with cpan

Syntax error near unexpected token '(' after implementing python program

QUESTION

Plotly-igraph plotting a tree with variable number of children nodes?

Asked 2021-Mar-02 at 11:45

I wish to generate a graph that visualizes the structure of an xml file.

I created a list of nodes to represent the xml file.
Each node contains 3 strings: the xml tag, attribute and content.

The xml file looks like this:

...

ANSWER

Answered 2021-Mar-02 at 11:45

You can create the graph like that:

Source https://stackoverflow.com/questions/66080452

QUESTION

How to import .OUT file into R?

Asked 2020-Jun-24 at 17:49

I have a file with the extension of .OUT; I can't seem to get it into R with its original column separations preserved.

Is there anyway I can read it into R without compromising its columns and rows?

The file can be found here: http://www.repeatmasker.org/PreMaskedGenomes.html ("hg19.fa.out.gz", the first one)

Thanks!

...

ANSWER

Answered 2020-Jun-24 at 17:49

Why don't you try using the read.fwf function:

https://stat.ethz.ch/R-manual/R-devel/library/utils/html/read.fwf.html

Source https://stackoverflow.com/questions/62560513

QUESTION

Can't locate Text/Soundex.pm in @INC

Asked 2019-Apr-21 at 16:55

I was installing repeatsmasker and it apparently seems to work because it shows "Congratulations! RepeatMasker is now ready to use." But when I run it it reports "Can't locate Text/Soundex.pm...". so I installed the module by "sudo cpan Text::Soundex", and by the end it tells me "Text::Soundex is up to date (3.05)." It seems the module is already installed, but RepeatMasker still has the same problem, as I'll show you in this code:

...

ANSWER

Answered 2019-Apr-21 at 16:55

You have two builds of Perl installed:

/usr/bin/perl
/home/fragua/anaconda/bin/perl.

/home/fragua/anaconda/bin/perl is first in your PATH. This means that programs with the following shebang (#!) line will use /home/fragua/anaconda/bin/perl:

Source https://stackoverflow.com/questions/55768847

QUESTION

Perl Module still not found after install with cpan

Asked 2017-Apr-20 at 16:42

I am having trouble getting a progam called RepeatMasker to work. I get following error:

...

ANSWER

Answered 2017-Apr-20 at 16:42

You've configured CPAN is installing the module in a non-standard location (/home/florian/perl5/lib/perl5), but you didn't tell Perl to look there for modules.

Source https://stackoverflow.com/questions/43523744

QUESTION

Syntax error near unexpected token '(' after implementing python program

Asked 2017-Mar-06 at 18:32

I initally ran RepeatMasker on a Mac, and I am attempting to analyze the file on a Linux OS.

When I try to run my program Unique_Repeat_Code.py:

...

ANSWER

Answered 2017-Mar-06 at 18:32

You are running your script as a bash script when you use the "./" syntax. You need to use the python interpreter to run your script:

Source https://stackoverflow.com/questions/42632827

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

Vulnerabilities

No vulnerabilities reported

Install RepeatMasker

You can download it from GitHub.

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 .

Find more information at: