perl-BioX-Seq-0.006004-alt1.noarch.rpm


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Description

perl-BioX-Seq - a (very) basic biological sequence object

Property Value
Distribution ALT Linux Sisyphus
Repository Autoimports noarch
Package name perl-BioX-Seq
Package version 0.006004
Package release alt1
Package architecture noarch
Package type rpm
Installed size 85.55 KB
Download size 85.55 KB
Official Mirror ftp.altlinux.org
`BioX::Seq' is a simple sequence class that can be used to represent
biological sequences. It was designed as a compromise between using simple
strings and hashes to hold sequences and using the rather bloated objects of
Bioperl. Features (or, depending on your viewpoint, bugs) include
auto-stringification and context-dependent transformations. It is meant
be used primarily as the return object of the `BioX::Seq::Fastx' parser, but
there may be occasions where it is useful in its own right.
`BioX::Seq' current implements a small subset of the transformations most
commonly used by the author (reverse complement, translate, subrange) - more
methods may be added in the future as use suggests and time permits, but the
core object will be kept as simple as possible and should be limited to the
four current properties - sequence, ID, description, and quality - that
satisfy 99% of the author's needs.
Some design decisions have been made for the sake of speed over ease of use.
For instance, there is no sanity-checking of the object properties upon
creation of a new object or use of the accessor methods. Parameters to the
constructor are positional rather than named (testing indicates that this
reduces execution times by ~ 40%).

Alternatives

Package Version Architecture Repository
perl-BioX-Seq - - -

Requires

Name Value
/usr/share/perl5 -
perl(Compress/BGZF/Reader.pm) -
perl(Cwd.pm) -
perl(File/Basename.pm) -
perl(File/Glob.pm) -
perl(File/Which.pm) -
perl(IO/Uncompress/Bunzip2.pm) -
perl(IO/Uncompress/Gunzip.pm) -
perl(POSIX.pm) -
perl(Scalar/Util.pm) -
perl(constant.pm) -
perl(overload.pm) -
perl-base >= 1:5.12.0
rpmlib(PayloadIsLzma) -

Provides

Name Value
perl(BioX/Seq.pm) = 0.006.004
perl(BioX/Seq/Fetch.pm) -
perl(BioX/Seq/Stream.pm) -
perl(BioX/Seq/Stream/FASTA.pm) -
perl(BioX/Seq/Stream/FASTQ.pm) -
perl(BioX/Seq/Stream/TwoBit.pm) -
perl(BioX/Seq/Utils.pm) -
perl-BioX-Seq = 0.006004-alt1

Download

Type URL
Binary Package perl-BioX-Seq-0.006004-alt1.noarch.rpm
Source Package perl-BioX-Seq-0.006004-alt1.src.rpm

Install Howto

  1. Add the following line to /etc/apt/sources.list:
    
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    rpm [Sisyphus] http://ftp.altlinux.org/pub/distributions/ALTLinux/autoimports/Sisyphus noarch autoimports
    
  2. Update the package index:
    # sudo apt-get update
  3. Install perl-BioX-Seq rpm package:
    # sudo apt-get install perl-BioX-Seq

Files

Path
/usr/share/doc/perl-BioX-Seq-0.006004/Changes
/usr/share/doc/perl-BioX-Seq-0.006004/LICENSE
/usr/share/doc/perl-BioX-Seq-0.006004/README.md
/usr/share/perl5/BioX/Seq.pm
/usr/share/perl5/BioX/Seq/Fetch.pm
/usr/share/perl5/BioX/Seq/Stream.pm
/usr/share/perl5/BioX/Seq/Utils.pm
/usr/share/perl5/BioX/Seq/Stream/FASTA.pm
/usr/share/perl5/BioX/Seq/Stream/FASTQ.pm
/usr/share/perl5/BioX/Seq/Stream/TwoBit.pm

See Also

Package Description
perl-BioX-SeqUtils-Promoter-0.1.1-alt1.noarch.rpm Identification of core promoter elements and CpG islands in DNA sequeces via Consensus Sequences/Mo
perl-BioX-SeqUtils-RandomSequence-0.94-alt1.noarch.rpm perl module BioX-SeqUtils-RandomSequence
perl-BioX-Workflow-1.10-alt1.noarch.rpm A very opinionated template based workflow writer
perl-BioX-Workflow-Plugin-Drake-0.12-alt1.noarch.rpm A very opinionated template based bioinformatics workflow writer for Drake
perl-BioX-Workflow-Plugin-ENV-0.01-alt1.noarch.rpm Export SAMPLE to ENV
perl-BioX-Workflow-Plugin-FileDetails-0.11-alt1.noarch.rpm Get metadata for files in directories processed by L<BioX::Workflow>
perl-BioX-Workflow-Plugin-FileDetails-scripts-0.11-alt1.noarch.rpm BioX-Workflow-Plugin-FileDetails scripts
perl-BioX-Workflow-Plugin-FileExists-0.13-alt1.noarch.rpm a plugin to BioX::Workflow
perl-BioX-Workflow-scripts-1.10-alt1.noarch.rpm BioX-Workflow scripts
perl-BioX-Wrapper-1.5-alt1.noarch.rpm Base class for BioX::Wrappers
perl-BioX-Wrapper-Gemini-0.05-alt1.noarch.rpm A simple wrapper around the python Gemini library for annotating VCF files
perl-BioX-Wrapper-Gemini-scripts-0.05-alt1.noarch.rpm BioX-Wrapper-Gemini scripts
perl-Bioinfo-0.1.11-alt1.noarch.rpm my perl module and CLIs for Biology
perl-Bioinfo-scripts-0.1.11-alt1.noarch.rpm Bioinfo scripts
perl-Bisect-Perl-UsingGit-0.33-alt1_19.noarch.rpm Help you to bisect Perl
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