GFFStrandLoc
Strand-Wise Gene and Protein Extraction from GFF3 Files
Description
Facilitates the extraction and organization of strand-specific genomic features from GFF3 files. In many species and variants, high quality genome annotations are not always available, necessitating de novo annotation using tools such as AUGUSTUS (Stanke et al., 2006; <doi:10.1093/nar/gkl200>). However, downstream processing of such annotations to obtain structured information, such as strand-wise gene locations, transcript regions, and associated protein identifiers—can be computationally intensive and complex. 'GFFStrandLoc' provides a streamlined framework to parse GFF3 files and generate structured outputs containing strand-wise and region-wise genomic coordinates for each transcript, along with their associated protein information. Additionally, it enables users to define custom promoter lengths and extract corresponding promoter region coordinates for genes in a strand-aware manner. By simplifying post-annotation processing, it enhances the usability of de novo annotated genomic datasets for downstream analysis and interpretation.
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| Flavor | Status |
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| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 4 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 16, 2026
Code
Structure
Lines of code
303
Files
6
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
0
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
No
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
–
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-15
Latest release
2026-04-15
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