From owner-svn-ports-all@freebsd.org Fri Sep 15 19:17:19 2017 Return-Path: Delivered-To: svn-ports-all@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 9D4F8E03C83; Fri, 15 Sep 2017 19:17:19 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org (repo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:0]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id 76C9C7447A; Fri, 15 Sep 2017 19:17:19 +0000 (UTC) (envelope-from sunpoet@FreeBSD.org) Received: from repo.freebsd.org ([127.0.1.37]) by repo.freebsd.org (8.15.2/8.15.2) with ESMTP id v8FJHIPH025048; Fri, 15 Sep 2017 19:17:18 GMT (envelope-from sunpoet@FreeBSD.org) Received: (from sunpoet@localhost) by repo.freebsd.org (8.15.2/8.15.2/Submit) id v8FJHIXH025043; Fri, 15 Sep 2017 19:17:18 GMT (envelope-from sunpoet@FreeBSD.org) Message-Id: <201709151917.v8FJHIXH025043@repo.freebsd.org> X-Authentication-Warning: repo.freebsd.org: sunpoet set sender to sunpoet@FreeBSD.org using -f From: Sunpoet Po-Chuan Hsieh Date: Fri, 15 Sep 2017 19:17:18 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r449922 - in head/biology: . p5-Bio-FeatureIO X-SVN-Group: ports-head X-SVN-Commit-Author: sunpoet X-SVN-Commit-Paths: in head/biology: . p5-Bio-FeatureIO X-SVN-Commit-Revision: 449922 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Fri, 15 Sep 2017 19:17:19 -0000 Author: sunpoet Date: Fri Sep 15 19:17:17 2017 New Revision: 449922 URL: https://svnweb.freebsd.org/changeset/ports/449922 Log: Add p5-Bio-FeatureIO 1.6.905 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. WWW: http://search.cpan.org/dist/Bio-FeatureIO/ Added: head/biology/p5-Bio-FeatureIO/ head/biology/p5-Bio-FeatureIO/Makefile (contents, props changed) head/biology/p5-Bio-FeatureIO/distinfo (contents, props changed) head/biology/p5-Bio-FeatureIO/pkg-descr (contents, props changed) head/biology/p5-Bio-FeatureIO/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Sep 15 18:48:38 2017 (r449921) +++ head/biology/Makefile Fri Sep 15 19:17:17 2017 (r449922) @@ -60,6 +60,7 @@ SUBDIR += p5-Bio-Coordinate SUBDIR += p5-Bio-Das SUBDIR += p5-Bio-Das-Lite + SUBDIR += p5-Bio-FeatureIO SUBDIR += p5-Bio-GFF3 SUBDIR += p5-Bio-Glite SUBDIR += p5-Bio-Graphics Added: head/biology/p5-Bio-FeatureIO/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-FeatureIO/Makefile Fri Sep 15 19:17:17 2017 (r449922) @@ -0,0 +1,28 @@ +# Created by: Po-Chuan Hsieh +# $FreeBSD$ + +PORTNAME= Bio-FeatureIO +PORTVERSION= 1.6.905 +CATEGORIES= biology perl5 +MASTER_SITES= CPAN +PKGNAMEPREFIX= p5- + +MAINTAINER= sunpoet@FreeBSD.org +COMMENT= Handler for FeatureIO + +LICENSE= ART10 GPLv1+ +LICENSE_COMB= dual +LICENSE_FILE= ${WRKSRC}/LICENSE + +BUILD_DEPENDS= p5-BioPerl>=0:biology/p5-BioPerl \ + p5-Tree-DAG_Node>=0:devel/p5-Tree-DAG_Node \ + p5-URI>=0:net/p5-URI \ + p5-XML-DOM>=0:textproc/p5-XML-DOM \ + p5-XML-DOM-XPath>=0:textproc/p5-XML-DOM-XPath +RUN_DEPENDS:= ${BUILD_DEPENDS} + +NO_ARCH= yes +USE_PERL5= configure +USES= perl5 + +.include Added: head/biology/p5-Bio-FeatureIO/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-FeatureIO/distinfo Fri Sep 15 19:17:17 2017 (r449922) @@ -0,0 +1,3 @@ +TIMESTAMP = 1505488503 +SHA256 (Bio-FeatureIO-1.6.905.tar.gz) = 322e5757b374f2fb90b8f20bdbdc75631f5cb4d122f81a4d35c3a177cf950c7a +SIZE (Bio-FeatureIO-1.6.905.tar.gz) = 54906 Added: head/biology/p5-Bio-FeatureIO/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-FeatureIO/pkg-descr Fri Sep 15 19:17:17 2017 (r449922) @@ -0,0 +1,19 @@ +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. + +WWW: http://search.cpan.org/dist/Bio-FeatureIO/ Added: head/biology/p5-Bio-FeatureIO/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/p5-Bio-FeatureIO/pkg-plist Fri Sep 15 19:17:17 2017 (r449922) @@ -0,0 +1,16 @@ +%%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