社区
下载资源悬赏专区
帖子详情
Bioinformatics with Python Cookbook下载
weixin_39820780
2019-09-18 04:30:53
非常适合生物信息领域的学习,与python结合。2015年6月出版,是找到的最新的python与生信结合的书本。
相关下载链接:
//download.csdn.net/download/woaielf/9296189?utm_source=bbsseo
...全文
54
回复
打赏
收藏
Bioinformatics with Python Cookbook下载
非常适合生物信息领域的学习,与python结合。2015年6月出版,是找到的最新的python与生信结合的书本。 相关下载链接://download.csdn.net/download/woaielf/9296189?utm_source=bbsseo
复制链接
扫一扫
分享
转发到动态
举报
AI
作业
写回复
配置赞助广告
用AI写文章
回复
切换为时间正序
请发表友善的回复…
发表回复
打赏红包
B
ioin
format
ics
with
Python
Cook
book
(PACKT,2015)
If you are either a computational biologist or a
Python
programmer, you will probably relate to the expression "explosive growth, exciting times".
Python
is arguably the main programming language for big data, and the deluge of data in biology, mostly from genom
ics
and proteom
ics
, makes b
ioin
format
ics
one of the most exciting fields in data science. Using the hands-on recipes in this
book
, you'll be able to do practical research and analysis in computational biology with
Python
. We cover modern, next-generation sequencing libraries and explore real-world examples on how to handle real data. The main focus of the
book
is the practical application of b
ioin
format
ics
, but we also cover modern programming techniques and frameworks to deal with the ever increasing deluge of b
ioin
format
ics
data.
B
ioin
format
ics
with
Python
Cook
book
非常适合生物信息领域的学习,与
python
结合。2015年6月出版,是找到的最新的
python
与生信结合的书本。
B
ioin
format
ics
with
Python
Cook
book
-Tiago Antao
B
ioin
format
ics
with
Python
Cook
book
_Tiago Antao
Python
for B
ioin
format
ics
第二版,最新版
最新的讲授将
Python
用于生物信息编程的书籍,希望大家喜欢。目录如下: Conventions 4 1.2.2
Python
Versions 5 1.2.3 Code Style 5 1.2.4 Get the Most from This
Book
without Reading It All 6 1.2.5 Online Resources Related to This
Book
7 1.3 WHY LEARN TO PROGRAM? 7 1.4 BASIC PROGRAMMING CONCEPTS 8 1.4.1 What Is a Program? 8 1.5 WHY
PYTHON
? 10 1.5.1 Main Features of
Python
10 1.5.2 Comparing
Python
with Other Languages 11 1.5.3 How Is It Used? 14 1.5.4 Who Uses
Python
? 15 1.5.5 Flavors of
Python
15 1.5.6 Special
Python
Distributions 16 1.6 ADDITIONAL RESOURCES 17 Chapter 2 First Steps with
Python
19 2.1 INSTALLING
PYTHON
20 2.1.1 Learn
Python
by Using It 20 2.1.2 Install
Python
Locally 20 2.1.3 Using
Python
Online 21 2.1.4 Testing
Python
22 2.1.5 First Use 22 2.2 INTERACTIVE MODE 23 2.2.1 Baby Steps 23 2.2.2 Basic Input and Output 23 2.2.3 More on the Interactive Mode 24 2.2.4 Mathematical Operations 26 2.2.5 Exit from the
Python
Shell 27 2.3 BATCH MODE 27 2.3.1 Comments 29 2.3.2 Indentation 30 2.4 CHOOSING AN EDITOR 32 2.4.1 Sublime Text 32 2.4.2 Atom 33 2.4.3 PyCharm 34 2.4.4 Spyder IDE 35 2.4.5 Final Words about Editors 36 2.5 OTHER TOOLS 36 2.6 ADDITIONAL RESOURCES 37 2.7 SELF-EVALUATION 37 Chapter 3 Basic Programming: Data Types 39 3.1 STRINGS 40 3.1.1 Strings Are Sequences of Unicode Characters 41 3.1.2 String Manipulation 42 3.1.3 Methods Associated with Strings 42 3.2 LISTS 44 3.2.1 Accessing List Elements 45 3.2.2 List with Multiple Repeated Items 45 3.2.3 List Comprehension 46 3.2.4 Modifying Lists 47 3.2.5 Copying a List 49 3.3 TUPLES 49 3.3.1 Tuples Are Immutable Lists 49 3.4 COMMON PROPERTIES OF THE SEQUENCES 51 3.5 DICTIONARIES 54 3.5.1 Mapping: Calling Each Value by a Name 54 3.5.2 Operating with Dictionaries 56 3.6 SETS 59 3.6.1 Unordered Collection of Objects 59 3.6.2 Set Operations 60 3.6.3 Shared Operations with Other Data Types 62 3.6.4 Immutable Set: Frozenset 63 3.7 NAMING OBJECTS 63 3.8 ASSIGNING A VALUE TO A VARIABLE VERSUS BINDING A NAME TO AN OBJECT 64 3.9 ADDITIONAL RESOURCES 67 3.10 SELF-EVALUATION 68 Chapter 4 Programming: Flow Control 69 4.1 IF-ELSE 69 4.1.1 Pass Statement 74 4.2 FOR LOOP 75 4.3 WHILE LOOP 77 4.4 BREAK: BREAKING THE LOOP 78 4.5 WRAPPING IT UP 80 4.5.1 Estimate the Net Charge of a Protein 80 4.5.2 Search for a Low-Degeneration Zone 81 4.6 ADDITIONAL RESOURCES 83 4.7 SELF-EVALUATION 83 Chapter 5 Handling Files 85 5.1 READING FILES 86 5.1.1 Example of File Handling 87 5.2 WRITING FILES 89 5.2.1 File Reading and Writing Examples 90 5.3 CSV FILES 90 5.4 PICKLE: STORING AND RETRIEVING THE CONTENTS OF VARI- ABLES 94 5.5 JSON FILES 96 5.6 FILE HANDLING: OS, OS.PATH, SHUTIL, AND PATH.PY MODULE 98 5.6.1 path.py Module 100 5.6.2 Consolidate Multiple DNA Sequences into One FASTA File 102 5.7 ADDITIONAL RESOURCES 102 5.8 SELF-EVALUATION 103 Chapter 6 Code Modularizing 105 6.1 INTRODUCTION TO CODE MODULARIZING 105 6.2 FUNCTIONS 106 6.2.1 Standard Way to Make
Python
Code Modular 106 6.2.2 Function Parameter Options 110 6.2.3 Generators 113 6.3 MODULES AND PACKAGES 114 6.3.1 Using Modules 115 6.3.2 Packages 116 6.3.3 Installing Third-Party Modules 117 6.3.4 Virtualenv: Isolated
Python
Environments 119 6.3.5 Conda: Anaconda Virtual Environment 121 6.3.6 Creating Modules 124 6.3.7 Testing Modules 125 6.4 ADDITIONAL RESOURCES 127 6.5 SELF-EVALUATION 128 Chapter 7 Error Handling 129 7.1 INTRODUCTION TO ERROR HANDLING 129 7.1.1 Try and Except 131 7.1.2 Exception Types 134 7.1.3 Triggering Exceptions 135 7.2 CREATING CUSTOMIZED EXCEPTIONS 136 7.3 ADDITIONAL RESOURCES 137 7.4 SELF-EVALUATION 138 Chapter 8 Introduction to Object Orienting Programming (OOP) 139 8.1 OBJECT PARADIGM AND
PYTHON
139 8.2 EXPLORING THE JARGON 140 8.3 CREATING CLASSES 142 8.4 INHERITANCE 145 8.5 SPECIAL METHODS 149 8.5.1 Create a New Data Type Using a Built-in Data Type 154 8.6 MAKING OUR CODE PRIVATE 154 8.7 ADDITIONAL RESOURCES 155 8.8 SELF-EVALUATION 156 Chapter 9 Introduction to Bio
python
157 9.1 WHAT IS BIO
PYTHON
? 158 9.1.1 Project Organization 158 9.2 INSTALLING BIO
PYTHON
159 9.3 BIO
PYTHON
COMPONENTS 162 9.3.1 Alphabet 162 9.3.2 Seq 163 9.3.3 MutableSeq 165 9.3.4 SeqRecord 166 9.3.5 Align 167 9.3.6 AlignIO 169 9.3.7 ClustalW 171 9.3.8 SeqIO 173 9.3.9 AlignIO 176 9.3.10 BLAST 177 9.3.11 Biological Related Data 187 9.3.12 Entrez 190 9.3.13 PDB 194 9.3.14 PROSITE 196 9.3.15 Restriction 197 9.3.16 SeqUtils 200 9.3.17 Sequencing 202 9.3.18 SwissProt 205 9.4 CONCLUSION 207 9.5 ADDITIONAL RESOURCES 207 9.6 SELF-EVALUATION 209 Section II Advanced Top
ics
Chapter 10 Web Applications 213 10.1 INTRODUCTION TO
PYTHON
ON THE WEB 213 10.2 CGI IN
PYTHON
214 10.2.1 Configuring a Web Server for CGI 215 10.2.2 Testing the Server with Our Script 215 10.2.3 Web Program to Calculate the Net Charge of a Protein (CGI version) 219 10.3 WSGI 221 10.3.1 Bottle: A
Python
Web Framework for WSGI 222 10.3.2 Installing Bottle 223 10.3.3 Minimal Bottle Application 223 10.3.4 Bottle Components 224 10.3.5 Web Program to Calculate the Net Charge of a Protein (Bottle Version) 229 10.3.6 Installing a WSGI Program in Apache 232 10.4 ALTERNATIVE OPTIONS FOR MAKING
PYTHON
-BASED DYNAMIC WEB SITES 232 10.5 SOME WORDS ABOUT SCRIPT SECURITY 232 10.6 WHERE TO HOST
PYTHON
PROGRAMS 234 10.7 ADDITIONAL RESOURCES 235 10.8 SELF-EVALUATION 236 Chapter 11 XML 237 11.1 INTRODUCTION TO XML 237 11.2 STRUCTURE OF AN XML DOCUMENT 241 11.3 METHODS TO ACCESS DATA INSIDE AN XML DOCUMENT 246 11.3.1 SAX: cElementTree Iterparse 246 11.4 SUMMARY 251 11.5 ADDITIONAL RESOURCES 252 11.6 SELF-EVALUATION 252 Chapter 12
Python
and Databases 255 12.1 INTRODUCTION TO DATABASES 256 12.1.1 Database Management: RDBMS 257 12.1.2 Components of a Relational Database 258 12.1.3 Database Data Types 260 12.2 CONNECTING TO A DATABASE 261 12.3 CREATING A MYSQL DATABASE 262 12.3.1 Creating Tables 263 12.3.2 Loading a Table 264 12.4 PLANNING AHEAD 266 12.4.1
Python
U: Sample Database 266 12.5 SELECT: QUERYING A DATABASE 269 12.5.1 Building a Query 271 12.5.2 Updating a Database 273 12.5.3 Deleting a Record from a Database 273 12.6 ACCESSING A DATABASE FROM
PYTHON
274 12.6.1 PyMySQL Module 274 12.6.2 Establishing the Connection 274 12.6.3 Executing the Query from
Python
275 12.7 SQLITE 276 12.8 NOSQL DATABASES: MONGODB 278 12.8.1 Using MongoDB with PyMongo 278 12.9 ADDITIONAL RESOURCES 282 12.10 SELF-EVALUATION 284 Chapter 13 Regular Expressions 285 13.1 INTRODUCTION TO REGULAR EXPRESSIONS (REGEX) 285 13.1.1 REGEX Syntax 286 13.2 THE RE MODULE 287 13.2.1 Compiling a Pattern 290 13.2.2 REGEX Examples 292 13.2.3 Pattern Replace 294 13.3 REGEX IN B
IOIN
FORMAT
ICS
294 13.3.1 Cleaning Up a Sequence 296 13.4 ADDITIONAL RESOURCES 297 13.5 SELF-EVALUATION 298 Chapter 14 Graph
ics
in
Python
299 14.1 INTRODUCTION TO BOKEH 299 14.2 INSTALLING BOKEH 299 14.3 USING BOKEH 301 14.3.1 A Simple X-Y Plot 303 14.3.2 Two Data Series Plot 304 14.3.3 A Scatter Plot 306 14.3.4 A Heatmap 308 14.3.5 A Chord Diagram 309 Section III
Python
Recipes with Commented Source Code Chapter 15 Sequence Manipulation in Batch 315 15.1 PROBLEM DESCRIPTION 315 15.2 PROBLEM ONE: CREATE A FASTA FILE WITH RANDOM SE- QUENCES 315 15.2.1 Commented Source Code 315 15.3 PROBLEM TWO: FILTER NOT EMPTY SEQUENCES FROM A FASTA FILE 316 15.3.1 Commented Source Code 317 15.4 PROBLEM THREE: MODIFY EVERY RECORD OF A FASTA FILE 319 15.4.1 Commented Source Code 320 Chapter 16 Web Application for Filtering Vector Contamination 321 16.1 PROBLEM DESCRIPTION 321 16.1.1 Commented Source Code 322 16.2 ADDITIONAL RESOURCES 326 Chapter 17 Searching for PCR Primers Using Primer3 329 17.1 PROBLEM DESCRIPTION 329 17.2 PRIMER DESIGN FLANKING A VARIABLE LENGTH REGION 330 17.2.1 Commented Source Code 331 17.3 PRIMER DESIGN FLANKING A VARIABLE LENGTH REGION, WITH BIO
PYTHON
332 17.4 ADDITIONAL RESOURCES 333 Chapter 18 Calculating Melting Temperature from a Set of Primers 335 18.1 PROBLEM DESCRIPTION 335 18.1.1 Commented Source Code 336 18.2 ADDITIONAL RESOURCES 336 Chapter 19 Filtering Out Specific Fields from a GenBank File 339 19.1 EXTRACTING SELECTED PROTEIN SEQUENCES 339 19.1.1 Commented Source Code 339 19.2 EXTRACTING THE UPSTREAM REGION OF SELECTED PRO- TEINS 340 19.2.1 Commented Source Code 340 19.3 ADDITIONAL RESOURCES 341 Chapter 20 Inferring Splicing Sites 343 20.1 PROBLEM DESCRIPTION 343 20.1.1 Infer Splicing Sites with Commented Source Code 345 20.1.2 Sample Run of Estimate Intron Program 347 Chapter 21 Web Server for Multiple Alignment 349 21.1 PROBLEM DESCRIPTION 349 21.1.1 Web Interface: Front-End. HTML Code 349 21.1.2 Web Interface: Server-Side Script. Commented Source Code 351 21.2 ADDITIONAL RESOURCES 353 Chapter 22 Drawing Marker Positions Using Data Stored in a Database 355 22.1 PROBLEM DESCRIPTION 355 22.1.1 Preliminary Work on the Data 355 22.1.2 MongoDB Version with Commented Source Code 358 Section IV Appendices
B
ioin
format
ics
-with-
Python
-
Cook
book
-Second-Edition:Packt出版的《
Python
手册第二版生物信息学》
《
Python
手册中的生物信息学》,第二版 这是Packt发行的代码库。 了解如何使用现代
Python
生物信息学库和应用程序进行计算生物学的前沿研究 这本书是关于什么的? 生物信息学是一个活跃的研究领域,它使用一系列简单而先进的计算来从生物数据中提取有价值的信息。 本书涵盖了下一代测序,基因组学,宏基因组学,种群遗传学,系统发育学和蛋白质组学。 您将学习现代的编程技术来分析大量的生物学数据。 借助实际示例,您将使用各种
Python
工具和库来转换,分析和可视化数据集。 本书涵盖以下激动人心的功能: 了解如何处理大型下一代测序(NGS)数据集 使用FASTQ,BAM和VCF格式处理基因组数据集 学习进行序列比较和系统发育重建 使用Protem
ics
数据执行复杂的分析 使用
Python
与Galaxy服务器进行交互 如果您觉得这本书适合您,请立即获取! 说明和导航 所有代码都组织在文件
下载资源悬赏专区
13,656
社区成员
12,674,760
社区内容
发帖
与我相关
我的任务
下载资源悬赏专区
CSDN 下载资源悬赏专区
复制链接
扫一扫
分享
社区描述
CSDN 下载资源悬赏专区
其他
技术论坛(原bbs)
社区管理员
加入社区
获取链接或二维码
近7日
近30日
至今
加载中
查看更多榜单
社区公告
暂无公告
试试用AI创作助手写篇文章吧
+ 用AI写文章