生物信息学 普通高等教育 “十二五”规划教材 生物信息学 Bioinformatics 第十一章：生物信息学编程基础
第十一章：生物信息学编程基础 普通高等教育 “十二五”规划教材 生物信息学 Bioinformatics
第一节Linux操作系统 一、Linuxi简介 二、Linux常用命令行操作 表11-1 Linux与DOS常用命令比较 Linux命令符 DOS命令符 功能 ls dir 显示文件及目录 ed ed 改变当前目录 mkdir md 新建目录 rmdir rd 删除目录 m del 删除文件 移动文件 复制文件 less type 阅读文件 echo echo 输出字符串
第一节 Linux操作系统 一、Linux简介 二、Linux常用命令行操作
第二节生物信息学中的编程语言 一、Perl 1、Perl简介 The Perl Programming Language www.perl.org HOME LEARN DOCUMENTATION CPAN COMMUNITY GET INVOLVED DOWNLOAD ABOUT PERL Current Perl version Flexible Powerful 5.18.1-download now That's why we love Perl 5 Find out more Learn Get started DOWNLOAD PERL Documentation Community Events Perl 5 is a highly capable,feature-rich programming language with over 25 years of development.More about why we love Perl... Database interfaces Learning Perl 5 The Perl Community DBIx:ass☒provides With free online books,over 25,000 Perl has an active world wide an Object Relational extension modules,and a large community with over 300 local Mapper (ORM)to developer community,there are groups,mailing lists and databases (e.g.Oracle, many ways to leam Perl 5. support/discussion websites SQL Server,MySQL, Postgress,Access etc) Documentation Contribute to Perl Sponsor Core documentation,FAQs and Perl is being actively developed. translations. There are many ways to get involved. phyber
第二节 生物信息学中的编程语言 一、Perl 1、Perl简介
2、Perl基础 数据类型： 字符串($string)、数组(@aray)、哈希表(%hash) 正则表达式 m//; 子程序 Sub SUBNAME { code; }
2、Perl基础 数据类型： 字符串($string)、数组(@array)、哈希表(%hash) 正则表达式 m//； 子程序 Sub SUBNAME { code; }
包 Package package1; 内置函数 abs、sqrt、exp 文件处理 open(FH,"path../filename"); 模块 LWP::Simple LWP:UserAgent DBI
包 Package package1； 内置函数 abs、sqrt、exp 文件处理 open(FH,”path../filename”); 模块 LWP::Simple LWP::UserAgent DBI
3、BioPerl概况 BioPerl是Perl的扩充，专门用于生物信息的工具与函数集。 表11-3 BioPerl模块说明 应用 模块 1.序列操作 对序列进行统计 SeqStats,Seq Word 确定限制性内切核酸酶位点 Bio::Restriction 识别氨基酸裂解位点 Sigcleave 多样性序列功能 OddCodes,SeqPattern 转换坐标系 Coordinate:Pair,RelSegment 2.搜索相似序列 运行远程BLAST using RemoteBlast.pm 分析BLAST和FASTA结果 Search,SearchIO 分析BLAST结果 BPlite,BPpsilite,and BPbl2seq 分析HMM结果 HMMER:Results,SearchIO 运行本地BLAST StandAloneBlast 3.序列比对 SimpleAlign 4.在基因组DNA寻找基因和其他结构 Genscan,Sim4,Grail,Genemark,ESTScan,MZEF,EPCR 5.开发机器可读性的序列注释 表征序列注释 SeqFeature,RichSeq,Location 表征序列注释 Annotation:Collection 表示大的序列 LargeSeq 表示改变的序列 LiveSeq
3、BioPerl概况 BioPerl是Perl的扩充，专门用于生物信息的工具与函数集
应用 模块 表示相关联的序列—一 突变体，多态性 Allele,SeqDiff 在序列注释中加入特征数据 Seq WithQuality 序列XML表征—生成和分析 SegIO:game,SegIO:bsml 使用GF℉表示序列 Bio:DB:GFF 6.操作序列簇 Cluster,ClusterIO 7.在BioPerl中表示非序列数据：结构、树和图谱 使用3D结构对象并读取PDB文件 StructureI,Structure::IO 树对象和系统发生树 Tree:Tree,TreelO,PAML 图谱对象操作遗传图谱 Map:MapI,MapIO 文献对象搜索文献数据库 Biblio 图形对象以图形代表序列对象 Graphics
二、Python 1、Python简介 python ABOUT 》 Python Programming Language-Official Website NEWS 》 Python is a programming language that lets you work more quickly and integrate your systems more effectively.You can learn to DOCUMENTATION see almost immediate gains in productivity and lower maintenance costs. DOWNLOAD Python runs on Windows,Linux/Unix,Mac OS X,and has been ported to the Java and NET virtual machines. 下载 COMMUNITY Python is free to use,even for commercial products,because of its OSl-approved open source license FOUNDATION 》 New to Python or choosing between Python 2 and Python 3?Read Python 2 or Python 3. CORE DEVELOPMENT》 Help The Python Software Foundation holds the intellectual property rights behind Python,underwrites the PyCon conference,and funds many Package Index Python community. Quick Links (2.7.5) Read more,-or-download Python now 》Documentation Windows Installer Python 3.4.0 alpha 4 has been released 》Source Distribution The fourth and final alpha for Python 3.4,Python 3.4.0a4,has been released. Quick Links (3.3.2) Published:Sun,20 October 2013,17:30-0700 >Documentation Python 2.6.9 release candidate 1 has been released 》Windows Installer The first release candidate for Python 2.6.9,Python 2.6.9rc1,has been released. 》Source Distribution Published:Mon,30 September 2013,21:12-0400 Python Jobs 201A PVTennessee Conference CFP
二、Python 1、Python简介
2、Python安装及开发运行环境的搭建 Windows: 7 Python 3.3.2 Shell 回X File Edit Shell Debug Options Windows Help Python3.3.2(v3.3.2:d047928ae3f6,May162013,00:06:53)[MsCv.160064bit(AH D64)]on win32 Type "copyright","credits"or "license()"for more information. >>print ('hello world') hello world >>> Linux: galaxy(mchen96G:~s python Python2.7.3(default,Ju152013,08:39:51) [GCC 4.6.3]on linux2 Type "help","copyright","credits"or "license"for more information. >>print 'hello world' hello world >>》>
2、Python安装及开发运行环境的搭建 Windows： Linux：
Python集成开发环境简介 IDLE Ipython Eclipse+pydev Ulipad Pyscripter Komodo和Komodo Edit WingIDE
Python集成开发环境简介 IDLE Ipython Eclipse+pydev Ulipad Pyscripter Komodo和Komodo Edit WingIDE