تسلط بر پایتون برای بیوانفورماتیک Mastering Python for Bioinformatics

فهرست مطالب:

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xi

Part I. The Rosalind.info Challenges

1. Tetranucleotide Frequency: Counting Things. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Getting Started 4

Creating the Program Using new.py 5

Using argparse 7

Tools for Finding Errors in the Code 10

Introducing Named Tuples 12

Adding Types to Named Tuples 15

Representing the Arguments with a NamedTuple 16

Reading Input from the Command Line or a File 18

Testing Your Program 20

Running the Program to Test the Output 23

Solution 1: Iterating and Counting the Characters in a String 25

Counting the Nucleotides 26

Writing and Verifying a Solution 28

Additional Solutions 30

Solution 2: Creating a count() Function and Adding a Unit Test 30

Solution 3: Using str.count() 34

Solution 4: Using a Dictionary to Count All the Characters 35

Solution 5: Counting Only the Desired Bases 38

Solution 6: Using collections.defaultdict() 39

Solution 7: Using collections.Counter() 41

Going Further 42

Review 42

2. Transcribing DNA into mRNA: Mutating Strings, Reading and Writing Files. . . . . . . . 45

Getting Started 46

Defining the Program’s Parameters 47

Defining an Optional Parameter 47

Defining One or More Required Positional Parameters 48

Using nargs to Define the Number of Arguments 49

Using argparse.FileType() to Validate File Arguments 49

Defining the Args Class 50

Outlining the Program Using Pseudocode 51

Iterating the Input Files 52

Creating the Output Filenames 52

Opening the Output Files 54

Writing the Output Sequences 55

Printing the Status Report 57

Using the Test Suite 57

Solutions 60

Solution 1: Using str.replace() 60

Solution 2: Using re.sub() 62

Benchmarking 64

Going Further 65

Review 65

3. Reverse Complement of DNA: String Manipulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

Getting Started 68

Iterating Over a Reversed String 70

Creating a Decision Tree 72

Refactoring 73

Solutions 74

Solution 1: Using a for Loop and Decision Tree 75

Solution 2: Using a Dictionary Lookup 75

Solution 3: Using a List Comprehension 78

Solution 4: Using str.translate() 78

Solution 5: Using Bio.Seq 81

Review 82

4. Creating the Fibonacci Sequence: Writing, Testing, and Benchmarking Algorithms. 83

Getting Started 84

An Imperative Approach 89

Solutions 91

Solution 1: An Imperative Solution Using a List as a Stack 91

Solution 2: Creating a Generator Function 93

Solution 3: Using Recursion and Memoization 96

Benchmarking the Solutions 100

Testing the Good, the Bad, and the Ugly 102

Running the Test Suite on All the Solutions 103

Going Further 109

Review 109

5. Computing GC Content: Parsing FASTA and Analyzing Sequences. . . . . . . . . . . . . . . . 111

Getting Started 112

Get Parsing FASTA Using Biopython 115

Iterating the Sequences Using a for Loop 118

Solutions 120

Solution 1: Using a List 120

Solution 2: Type Annotations and Unit Tests 123

Solution 3: Keeping a Running Max Variable 127

Solution 4: Using a List Comprehension with a Guard 129

Solution 5: Using the filter() Function 130

Solution 6: Using the map() Function and Summing Booleans 130

Solution 7: Using Regular Expressions to Find Patterns 131

Solution 8: A More Complex find_gc() Function 132

Benchmarking 134

Going Further 134

Review 135

6. Finding the Hamming Distance: Counting Point Mutations. . . . . . . . . . . . . . . . . . . . . 137

Getting Started 138

Iterating the Characters of Two Strings 141

Solutions 142

Solution 1: Iterating and Counting 142

Solution 2: Creating a Unit Test 143

Solution 3: Using the zip() Function 145

Solution 4: Using the zip_longest() Function 147

Solution 5: Using a List Comprehension 148

Solution 6: Using the filter() Function 149

Solution 7: Using the map() Function with zip_longest() 150

Solution 8: Using the starmap() and operator.ne() Functions 151

Going Further 153

Review 153

7. Translating mRNA into Protein: More Functional Programming. . . . . . . . . . . . . . . . . 155

Getting Started 155

K-mers and Codons 157

Translating Codons 160

Solutions 161

Solution 1: Using a for Loop 161

Solution 2: Adding Unit Tests 162

Solution 3: Another Function and a List Comprehension 165

Solution 4: Functional Programming with the map(), partial(), and

takewhile() Functions 167

Solution 5: Using Bio.Seq.translate() 169

Benchmarking 170

Going Further 170

Review 170

8. Find a Motif in DNA: Exploring Sequence Similarity. . . . . . . . . . . . . . . . . . . . . . . . . . . . 171

Getting Started 171

Finding Subsequences 173

Solutions 175

Solution 1: Using the str.find() Method 176

Solution 2: Using the str.index() Method 177

Solution 3: A Purely Functional Approach 179

Solution 4: Using K-mers 181

Solution 5: Finding Overlapping Patterns Using Regular Expressions 183

Benchmarking 184

Going Further 185

Review 185

9. Overlap Graphs: Sequence Assembly Using Shared K-mers. . . . . . . . . . . . . . . . . . . . . . 187

Getting Started 188

Managing Runtime Messages with STDOUT, STDERR, and Logging 192

Finding Overlaps 195

Grouping Sequences by the Overlap 196

Solutions 200

Solution 1: Using Set Intersections to Find Overlaps 200

Solution 2: Using a Graph to Find All Paths 203

Going Further 208

Review 208

10. Finding the Longest Shared Subsequence: Finding K-mers, Writing Functions, and

Using Binary Search. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211

Getting Started 211

Finding the Shortest Sequence in a FASTA File 213

Extracting K-mers from a Sequence 215

Solutions 217

Solution 1: Counting Frequencies of K-mers 217

Solution 2: Speeding Things Up with a Binary Search 220

Going Further 226

Review 226

11. Finding a Protein Motif: Fetching Data and Using Regular Expressions. . . . . . . . . . . 227

Getting Started 227

Downloading Sequences Files on the Command Line 230

Downloading Sequences Files with Python 233

Writing a Regular Expression to Find the Motif 235

Solutions 237

Solution 1: Using a Regular Expression 237

Solution 2: Writing a Manual Solution 239

Going Further 244

Review 244

12. Inferring mRNA from Protein: Products and Reductions of Lists. . . . . . . . . . . . . . . . . 245

Getting Started 245

Creating the Product of Lists 247

Avoiding Overflow with Modular Multiplication 249

Solutions 251

Solution 1: Using a Dictionary for the RNA Codon Table 251

Solution 2: Turn the Beat Around 257

Solution 3: Encoding the Minimal Information 259

Going Further 260

Review 261

13. Location Restriction Sites: Using, Testing, and Sharing Code. . . . . . . . . . . . . . . . . . . . 263

Getting Started 264

Finding All Subsequences Using K-mers 266

Finding All Reverse Complements 267

Putting It All Together 267

Solutions 268

Solution 1: Using the zip() and enumerate() Functions 268

Solution 2: Using the operator.eq() Function 270

Solution 3: Writing a revp() Function 271

Testing the Program 272

Going Further 274

Review 274

14. Finding Open Reading Frames. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275

Getting Started 275

Translating Proteins Inside Each Frame 277

Finding the ORFs in a Protein Sequence 279

Solutions 280

Solution 1: Using the str.index() Function 280

Solution 2: Using the str.partition() Function 282

Solution 3: Using a Regular Expression 284

Going Further 286

Review 286

Part II. Other Programs

15. Seqmagique: Creating and Formatting Reports. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 289

Using Seqmagick to Analyze Sequence Files 290

Checking Files Using MD5 Hashes 291

Getting Started 293

Formatting Text Tables Using tabulate() 295

Solutions 296

Solution 1: Formatting with tabulate() 296

Solution 2: Formatting with rich 303

Going Further 305

Review 306

16. FASTX grep: Creating a Utility Program to Select Sequences. . . . . . . . . . . . . . . . . . . . 307

Finding Lines in a File Using grep 308

The Structure of a FASTQ Record 308

Getting Started 311

Guessing the File Format 315

Solution 317

Going Further 327

Review 327

17. DNA Synthesizer: Creating Synthetic Data with Markov Chains. . . . . . . . . . . . . . . . . . 329

Understanding Markov Chains 329

Getting Started 332

Understanding Random Seeds 335

Reading the Training Files 337

Generating the Sequences 340

Structuring the Program 343

Solution 343

Going Further 347

Review 347

18. FASTX Sampler: Randomly Subsampling Sequence Files. . . . . . . . . . . . . . . . . . . . . . . . 349

Getting Started 349

Reviewing the Program Parameters 350

Defining the Parameters 352

Nondeterministic Sampling 354

Structuring the Program 356

Solutions 356

Solution 1: Reading Regular Files 357

Solution 2: Reading a Large Number of Compressed Files 358

Going Further 360

Review 360

19. Blastomatic: Parsing Delimited Text Files. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 361

Introduction to BLAST 361

Using csvkit and csvchk 364

Getting Started 368

Defining the Arguments 371

Parsing Delimited Text Files Using the csv Module 373

Parsing Delimited Text Files Using the pandas Module 377

Solutions 383

Solution 1: Manually Joining the Tables Using Dictionaries 383

Solution 2: Writing the Output File with csv.DictWriter() 384

Solution 3: Reading and Writing Files Using pandas 385

Solution 4: Joining Files Using pandas 387

Going Further 390

Review 390

A. Documenting Commands and Creating Workflows with make. . . . . . . . . . . . . . . . . . . . 391

B. Understanding $PATH and Installing Command-Line Programs. . . . . . . . . . . . . . . . . . 405

Epilogue. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 409

Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 411

مشخصات فایل

عنوان (Title):	Mastering Python for Bioinformatics_ How to Write Flexible, Documented, Tested Python Code for Research Computing-O'Reilly Media
نام فایل (File name):	603-www.GeneProtocols.ir-Mastering Python for Bioinformatics_ How to Write Flexible, Documented, Tested Python Code for Research Computing-O'Reilly Media (2021).pdf
عنوان فارسی (Title in Persian):	تسلط بر پایتون برای بیوانفورماتیک_ نحوه نوشتن کد های انعطاف پذیر، مستند و آزمایش شده پایتون برای محاسبات تحقیقاتی
ایجاد کننده:	Ken Youens-Clark
زبان (Language):	انگلیسی English
سال انتشار:	2021
شابک ISBN:	1098100883, 9781098100889
نوع سند (Doc. type):	کتاب
فرمت (File extention):	PDF
حجم فایل (File size):	10.3
تعداد صفحات (Book length in pages):	458