BSD Portsbiology/py-pyfaidx 0.5.9.5_1 DragonFly
Efficient pythonic random access to fasta subsequences
- System
- DragonFly
- Repository
- DPorts
- Maintainer
- [email protected] (as in FreeBSD)
- License
- BSD3CLAUSE
- Categories
- biology, python
- Package size
- 49.5 KiB, 264.4 KiB installed
Description
FASTA is a format to exchange generic information, partial or of the entire organism.
A function "faidx" (FAsta InDeX) creates a small flat index file ".fai" allowing for fast random access to any subsequence in the indexed FASTA file, while loading a minimal amount of the file in to memory. This python module implements pure Python classes for indexing, retrieval, and in-place modification of FASTA files using a samtools compatible index. The pyfaidx module is API compatible with the pygr seqdb module. A command-line script "faidx" is installed alongside the pyfaidx module, and facilitates complex manipulation of FASTA files without any programming knowledge.
In the other systems
The newest version among them is 0.9.1, as upstream numbers it.
| System | Port | Version | Vulnerabilities | Status | Maintainer | Last update |
|---|---|---|---|---|---|---|
| DragonFly | biology/py-pyfaidx | 0.5.9.5_1 behind since 2026-10-22 | none known | - | [email protected] | - |
| FreeBSD | biology/py-pyfaidx | 0.9.1 newest | none known | - | [email protected] | 2026-10-22 |
| HardenedBSD | biology/py-pyfaidx | 0.9.0.4 behind since 2026-10-22 | no data | - | [email protected] | - |
| GhostBSD | biology/py-pyfaidx | 0.9.0.4 behind since 2026-10-22 | no data | - | [email protected] | - |
Install
Binary package:
pkg install py311-pyfaidxFrom DPorts:
cd /usr/dports/biology/py-pyfaidx && make install cleanDependency graph
Ports that need it on the left, what it needs to run on the right; at most 8 of each. "Dependencies" below lists them all.