BSD Ports

biology/p5-Bio-FeatureIO 1.6.905 FreeBSD

Handler for FeatureIO

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
License
ART10, GPLv1+
Categories
biology, perl5
Package size
56.2 KiB, 159.5 KiB installed

Description

Bio::FeatureIO is an iterator subsystem for genomic sequence features.

Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg, Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the format objects, which most people should use.

The Bio::FeatureIO system can be thought of like biological file handles. They are attached to filehandles with smart formatting rules (eg, GFF format, or BED format) and can either read or write feature objects (Bio::SeqFeature objects, or more correctly, Bio::FeatureHolderI implementing objects, of which Bio::SeqFeature is one such object). If you want to know what to do with a Bio::SeqFeatureI object, read Bio::SeqFeatureI.

The idea is that you request a stream object for a particular format. All the stream objects have a notion of an internal file that is read from or written to. A particular FeatureIO object instance is configured for either input or output. A specific example of a stream object is the Bio::FeatureIO::gff object.

In the other systems

SystemPortVersion
FreeBSDbiology/p5-Bio-FeatureIO1.6.905
DragonFlybiology/p5-Bio-FeatureIO1.6.905
HardenedBSDbiology/p5-Bio-FeatureIO1.6.905
GhostBSDbiology/p5-Bio-FeatureIO1.6.905

Install

Binary package:

pkg install p5-Bio-FeatureIO

From the ports tree:

cd /usr/ports/biology/p5-Bio-FeatureIO/ && make install clean

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

RUN_DEPENDS=	p5-Bio-FeatureIO>0:biology/p5-Bio-FeatureIO

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:latest1.6.9051.6.9051.6.9051.6.9051.6.905
FreeBSD:14:quarterly1.6.9051.6.905n/a1.6.9051.6.905
FreeBSD:15:latest1.6.9051.6.905n/a1.6.9051.6.905
FreeBSD:15:quarterly1.6.9051.6.905n/an/an/a
FreeBSD:16:latest1.6.9051.6.905n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 5

Runtime 5

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

Build dependencies 79
Run dependencies 79
Required by 1

Configuration

No options to configure.

USES
perl5
Service scripts
none

Files

pkg-plist 16
  • %%SITE_PERL%%/Bio/FeatureIO.pm
  • %%SITE_PERL%%/Bio/FeatureIO/bed.pm
  • %%SITE_PERL%%/Bio/FeatureIO/gff.pm
  • %%SITE_PERL%%/Bio/FeatureIO/gtf.pm
  • %%SITE_PERL%%/Bio/FeatureIO/interpro.pm
  • %%SITE_PERL%%/Bio/FeatureIO/ptt.pm
  • %%SITE_PERL%%/Bio/FeatureIO/vecscreen_simple.pm
  • %%SITE_PERL%%/Bio/SeqFeature/Annotated.pm
  • %%PERL5_MAN3%%/Bio::FeatureIO.3.gz
  • %%PERL5_MAN3%%/Bio::FeatureIO::bed.3.gz
  • %%PERL5_MAN3%%/Bio::FeatureIO::gff.3.gz
  • %%PERL5_MAN3%%/Bio::FeatureIO::gtf.3.gz
  • %%PERL5_MAN3%%/Bio::FeatureIO::interpro.3.gz
  • %%PERL5_MAN3%%/Bio::FeatureIO::ptt.3.gz
  • %%PERL5_MAN3%%/Bio::FeatureIO::vecscreen_simple.3.gz
  • %%PERL5_MAN3%%/Bio::SeqFeature::Annotated.3.gz
distinfo 1
FileSizeSHA256
Bio-FeatureIO-1.6.905.tar.gz54906322e5757b374f2fb90b8f20bdbdc75631f5cb4d122f81a4d35c3a177cf950c7a
Master sites 1
  • CPAN

Commit history 0

No commits in the history this site was built from.