bioawk | BWK awk modified for biological data | Genomics library

by lh3 C Version: v1.0 License: No License

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kandi X-RAY | bioawk Summary

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

Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few built-in functions and an command line option to use TAB as the input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk. The original awk requires a YACC-compatible parser generator (e.g. Byacc or Bison). Bioawk further depends on zlib so as to work with gzip'd files.

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Support

bioawk has a low active ecosystem.

It has 476 star(s) with 104 fork(s). There are 35 watchers for this library.

It had no major release in the last 12 months.

There are 17 open issues and 12 have been closed. On average issues are closed in 212 days. There are 3 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of bioawk is v1.0

Quality

bioawk has 0 bugs and 0 code smells.

Security

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

bioawk code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

bioawk does not have a standard license declared.

Check the repository for any license declaration and review the terms closely.

Without a license, all rights are reserved, and you cannot use the library in your applications.

Reuse

bioawk releases are available to install and integrate.

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

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bioawk Key Features

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bioawk Examples and Code Snippets

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Community Discussions

Trending Discussions on bioawk

Select sequences in a fasta file with more than 300 aa and "C" occurs at least 4 times

QUESTION

Select sequences in a fasta file with more than 300 aa and "C" occurs at least 4 times

Asked 2018-Oct-08 at 14:59

I have a fasta file which contains protein sequences. I'd like to select sequences with more than 300 amino acids and Cysteine (C) amino acid appears more than 4 times.

I've used this command to select sequences with more than 300 aa:

...

ANSWER

Answered 2018-Oct-08 at 14:59

I do not know bioawk but I assume it is identical to awk with some initial parsing and constant definitions.

I would proceed as follows. Assuming you want the find the strings with more then 4 times the letter C in and a length of more than 300, then you could do :

Source https://stackoverflow.com/questions/50214546

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

Vulnerabilities

No vulnerabilities reported

Install bioawk

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 .

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