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/
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implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:
Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
* "Binned bitsets" which act just like chromosome sized bit arrays,
but lazily allocate regions and allow large blocks of all set or
all unset bits to be stored compactly
* "Intersecter" for performing fast intersection tests that preserve
both query and target intervals and associated annotation
WWW: https://github.com/bxlab/bx-python
PR: 218757
Submitted by: Yuri Victorovich <yuri@rawbw.com>
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access
to the command line functionality of the samtools and bcftools packages. The
module supports compression and random access through indexing.
This module provides a low-level wrapper around the htslib C-API as using
cython and a high-level API for convenient access to the data within standard
genomic file formats.
WWW: https://pypi.python.org/pypi/pysam
PR: 218745
Submitted by: Yuri Victorovich <yuri@rawbw.com>
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Bio::Coordinate classes are used for working with various biological coordinate
systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
WWW: http://search.cpan.org/dist/Bio-Coordinate/
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biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage
PR: 204127
Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data.
This port contains applications built on SeqAn and developed
within the SeqAn project. Among them are famous read mappers
like RazerS and Yara, as well as many other tools. Some
applications are packaged seperately and the library
can be found at biology/seqan.
WWW: http://www.seqan.de/
PR: 204127
Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.
The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.
WWW: http://biom-format.org/
PR: 209193
Submitted by: Joseph Mingrone
alignment mode). The speedup over BLAST is up to 20,000 on short reads at a
typical sensitivity of 90-99% relative to BLAST depending on the data and
settings.
WWW: http://ab.inf.uni-tuebingen.de/software/diamond/
PR: 208998
Submitted by: jrm@ftfl.ca
A k-mer is a substring of length k, and counting the occurrences of all such
substrings is a central step in many analyses of DNA sequence. JELLYFISH can
count k-mers quickly by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase parallelism.
WWW: http://www.genome.umd.edu/jellyfish.html
PR: 207929
Submitted by: bacon4000@gmail.com
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
This is Bowtie version 2, which will need to coexists with Bowtie 1 for the
foreseeable future. Both are required by certain genomics pipelines, in some
cases (e.g. Trinity) by the same pipeline.
WWW: https://github.com/BenLangmead/bowtie2
PR: 207908
Submitted by: Jason Bacon <bacon4000@gmail.com>
Slclust is a utility that performs single-linkage clustering with the option of
applying a Jaccard similarity coefficient to break weakly bound clusters into
distinct clusters.
WWW: http://sourceforge.net/projects/slclust/
PR: 207997
Submitted by: Jason Bacon <bacon4000@gmail.com>
TransDecoder identifies candidate coding regions within transcript
sequences, such as those generated by de novo RNA-Seq transcript
assembly using Trinity, or constructed based on RNA-Seq alignments
to the genome using Tophat and Cufflinks.
WWW: http://transdecoder.github.io/
PR: 207993
Submitted by: Jason Bacon <bacon4000@gmail.com>
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.
WWW: http://bowtie-bio.sourceforge.net/index.shtml
PR: 206939
Submitted by: Jason Bacon <bacon4000@gmail.com>
A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.
WWW: https://github.com/vcftools/vcftools
PR: 206926
Submitted by: Jason Bacon <bacon4000@gmail.com>
genomics analysis tasks. The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome. For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.
WWW: http://bedtools.readthedocs.org/
PR: 204536
Submitted by: scottcheloha@gmail.com
2015-11-26 audio/pecl-id3: Broken for more than 6 months
2015-11-26 dns/geta: Broken for more than 6 months
2015-11-26 finance/openerp-web: Broken for more than 6 months
2015-11-26 devel/py-async: Further using of this module is not encouraged by upstream
2015-11-26 chinese/kon2: Depends on expiring chinese/cce
2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi
2015-11-26 archivers/wzip: Broken for more than 6 months
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2015-11-27 www/mediawiki119: Please upgrade to mediawiki-1.25
2015-11-28 www/R-cran-Rpad: Unmaintained upstream
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.
WWW: http://sourceforge.net/projects/bio-bwa/
PR: 203158
Submitted by: Jason Bacon <jwbacon@tds.net>
alignments of nucleotide or protein sequences. FastTree can handle alignments
with up to a million of sequences in a reasonable amount of time and memory.
WWW: http://www.microbesonline.org/fasttree/
PR: 203295
Submitted by: Jason Bacon <jwbacon@tds.net>
BCFtools is a set of utilities that manipulate variant calls in the
Variant Call Format (VCF) and its binary counterpart BCF. All
commands work transparently with both VCFs and BCFs, both
uncompressed and BGZF-compressed.
WWW: http://www.htslib.org/
PR: 199747
Submitted by: cartwright@asu.edu
2015-01-01 biology/boinc-simap: Project shutting down, see http://boincsimap.org/boincsimap/forum_thread.php?id=88
2015-01-01 security/openssh-portable-base: Overwrite-base option/port/pkg will be removed. There is no real need for foot-shooting.
2015-01-01 devel/cedet: Fails to build, use Emacs' builtin cedet package instead
2015-01-01 devel/ecb: does not work with newer Emacs versions, use the elpa package instead
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
WWW: http://www.htslib.org/
PR: 195592
Submitted by: Reed A. Cartwright <cartwright@asu.edu>
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.
WWW: http://www.htslib.org/
PR: 195591
Submitted by: Reed A. Cartwright <cartwright@asu.edu>
PR: 190854
Submitted by: Jason Bacon
The Basic Local Alignment Search Tool (BLAST) finds regions of local
similarity between sequences. The program compares nucleotide or protein
sequences to sequence databases and calculates the statistical
significance of matches. BLAST can be used to infer functional and
evolutionary relationships between sequences as well as help identify
members of gene families.
2014-04-16 ports-mgmt/pkgsearch: Upstream disappeared
2014-04-17 science/flounder: Unmaintained since 2002
2014-04-17 security/nbaudit: Unmaintained since 2002
2014-04-17 security/saint: Unmaintained since 2002
2014-04-17 graphics/gozer: Unmaintained since 2002
2014-04-17 misc/pdfmap: Unmaintained since 2002
2014-04-17 devel/showgrammar: Unmaintained since 2002
2014-04-17 biology/libgenome: Unmaintained since 2002
2014-04-17 deskutils/narval: Unmaintained since 2002
2014-04-17 devel/fampp: Unmaintained since 2002
2014-04-17 net-p2p/py-fngrab: Unmaintained since 2002
2014-04-17 misc/wmfirew: Unmaintained since 2002
2014-04-17 x11-wm/e16utils: Unmaintained since 2002
2014-04-17 misc/salias: Unmaintained since 2002
2014-04-17 print/latex2slides: Unmaintained since 2002
2014-04-17 lang/sxm: Unmaintained since 2002
2014-04-17 textproc/pybook: Unmaintained since 2002
2014-04-17 mail/mailcrypt: Unmaintained since 2002
2014-04-17 japanese/elvis: Unmaintained since 2002
2014-04-17 devel/prototype: Unmaintained since 2002
2014-04-17 print/wprint: Unmaintained since 2002
2014-04-17 science/euler: Unmaintained since 2002
2014-04-17 multimedia/gopchop: Unmaintained since 2002
2014-04-17 science/gdis: Unmaintained since 2002
2014-04-17 net/googolplex: Unmaintained since 2002
2014-04-17 lang/logo: Unmaintained since 2002
2014-04-17 textproc/roap: Unmaintained since 2002
2014-04-17 x11-wm/afterstep-i18n: Unmaintained since 2002
2014-04-17 games/yamsweeper: Unmaintained since 2002
2014-04-17 net-mgmt/echolot: Unmaintained since 2002
2014-04-17 security/pam_smb: Unmaintained since 2002
2014-04-18 devel/lua-redis-parser: Broken for more than 6 months
2014-04-18 biology/finchtv: Broken for more than 6 months
2014-04-18 net-im/ari-yahoo: Broken for more than 1 year (http://www.icculus.org/ari-yahoo/)
