BSD Ports

biology/py-pyfaidx 0.9.1 FreeBSD

Efficient pythonic random access to fasta subsequences

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
a9b65ec92e
License
BSD3CLAUSE
Categories
biology, python
Package size
61.7 KiB, 289.8 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

SystemPortVersion
FreeBSDbiology/py-pyfaidx0.9.1
DragonFlybiology/py-pyfaidx0.5.9.5_1
HardenedBSDbiology/py-pyfaidx0.9.0.4
GhostBSDbiology/py-pyfaidx0.9.0.4

Install

Binary package:

pkg install py312-pyfaidx

From the ports tree:

cd /usr/ports/biology/py-pyfaidx/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	py312-pyfaidx>0:biology/py-pyfaidx

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest0.9.0.40.9.0.40.5.9.50.5.9.5_10.9.0.4
FreeBSD:14:quarterly0.9.0.40.9.0.4n/a0.5.9.5_10.9.0.4
FreeBSD:15:latest0.9.0.40.9.0.4n/a0.5.9.5_10.5.9.5_1
FreeBSD:15:quarterly0.9.0.40.9.0.4n/an/an/a
FreeBSD:16:latest0.9.0.40.9.0.4n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 3

Runtime 1

The full lists below include those, and their dependencies in turn.

Build dependencies 17
Run dependencies 11
Required by 1

Configuration

No options to configure.

USES
python
Service scripts
none

Files

distinfo 1
FileSizeSHA256
pyfaidx-0.9.1.tar.gz73553d84fa3bc90d48211101b509934431b00c0ac32de6513f7f348b90687135cc6ef
Master sites 1
  • PYPI

Commit history 1

DateCommitCreditsLog message
a9b65ec92e Yuri Victorovich biology/py-pyfaidx: update 0.9.0.4 → 0.9.1