| Port details on branch 2022Q2 |
- py-pyfaidx Efficient pythonic random access to fasta subsequences
- 0.5.9.5 biology
 =0      0.5.9.5Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2018-10-19 02:05:49
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- Also Listed In: python
- License: BSD3CLAUSE
- WWW:
- https://github.com/mdshw5/pyfaidx
- 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.
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- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - There is no configure plist information for this port.
- Dependency lines:
-
- ${PYTHON_PKGNAMEPREFIX}pyfaidx>0:biology/py-pyfaidx@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/py-pyfaidx/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/py-pyfaidx
- pkg install py39-pyfaidx
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py39-pyfaidx listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-pyfaidx
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1619213645
SHA256 (pyfaidx-0.5.9.5.tar.gz) = 9965644c5bd62bedc0ff7f336cbb2baef6406a36b4ec5c786b199872ce46192b
SIZE (pyfaidx-0.5.9.5.tar.gz) = 32772
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-six>0 : devel/py-six@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- biology/py-gffutils
Configuration Options:- No options to configure
- Options name:
- biology_py-pyfaidx
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
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