Managing Your Biological Data with Python

Content: Getting Started The Python Shell  In This Chapter You Will Learn  Story: Calculating the DELTAG of ATP Hydrolysis  What Do the Commands Mean?  Examples  Testing Yourself   Your First Python Program  In This Chapter You Will Learn  Story: How to Calculate the Frequency of Amino Acids from Insulin What Do the Commands Mean?  Examples  Testing Yourself   Data Management Analyzing a Data Column  In This Chapter You Will Learn  Story: Dendritic Lengths  What Do the Commands Mean?  Examples  Testing Yourself   Parsing Data Records  In This Chapter You Will Learn  Story: Integrating Mass Spectrometry Data into Metabolic Pathways What Do the Commands Mean?  Examples  Testing Yourself   Searching Data In This Chapter You Will Learn  Story: Translating an RNA Sequence into the Corresponding Protein Sequence What Do the Commands Mean?  Examples  Testing Yourself   Filtering Data In This Chapter You Will Learn  Story: Working with RNA-Seq Output Data What Do the Commands Mean?  Examples  Testing Yourself   Managing Tabular Data In This Chapter You Will Learn  Story: Determining Protein Concentrations What Do the Commands Mean?  Examples  Testing Yourself   Sorting Data In This Chapter You Will Learn  Story: Sort a Data Table What Do the Commands Mean?  Examples  Testing Yourself   Pattern Matching and Text Mining In This Chapter You Will Learn  Story: Search a Phosphorylation Motif in a Protein Sequence What Do the Commands Mean?  Examples  Testing Yourself   Modular Programming Divide a Program into Functions In This Chapter You Will Learn  Story: Working with Three-Dimensional Coordinate Files What Do the Commands Mean?  Examples  Testing Yourself   Managing Complexity with Classes In This Chapter You Will Learn  Story: Mendelian Inheritance What Do the Commands Mean?  Examples  Testing Yourself   Debugging In This Chapter You Will Learn  Story: When Your Program Does Not Work What Do the Commands Mean?  Examples  Testing Yourself   Using External Modules: The Python Interface to R In This Chapter You Will Learn  Story: Reading Numbers from a File and Calculating Their Mean Value Using R with Python What Do the Commands Mean?  Examples  Testing Yourself   Building Program Pipelines In This Chapter You Will Learn  Story: Building an NGS Pipeline What Do the Commands Mean?  Examples  Testing Yourself   Writing Good Programs In This Chapter You Will Learn  Problem Description: Uncertainty What Do the Commands Mean?  Examples  Testing Yourself   Data Visualization Creating Scientific Diagrams In This Chapter You Will Learn  Story: Nucleotide Frequencies in the Ribosome What Do the Commands Mean?  Examples  Testing Yourself   Creating Molecule Images with PyMOL In This Chapter You Will Learn  Story: The Zinc Finger Seven Steps to Create a High-Resolution Image Examples  Testing Yourself   Manipulating Images In This Chapter You Will Learn  Story: Plot a Plasmid What Do the Commands Mean?  Examples  Testing Yourself   Biopython Working with Sequence Data In This Chapter You Will Learn  Story: How to Translate a DNA Coding Sequence into the Corresponding Protein Sequence and Write It to a FASTA File What Do the Commands Mean?  Examples  Testing Yourself   Retrieving Data from Web Resources In This Chapter You Will Learn  Story: Searching Publications by Keywords in PubMed, Downloading the Corresponding Records, and Writing Papers Published in a Given Year to a File What Do the Commands Mean?  Examples  Testing Yourself   Working with 3D Structure Data In This Chapter You Will Learn  Story: Extracting Atom Names and Three-Dimensional Coordinates from a PDB File What Do the Commands Mean?  Examples  Testing Yourself   Cookbook Recipe 1: The PyCogent Library  Recipe 2: Reversing and Randomizing a Sequence Recipe 3: Creating a Random Sequence with Probabilities  Recipe 4: Parsing Multiple Sequence Alignments Using Biopython  Recipe 5: Calculating a Consensus Sequence from a Multiple Sequence Alignment  Recipe 6: Calculating the Distance between Phylogenetic Tree Nodes  Recipe 7: Codon Frequencies in a Nucleotide Sequence  Recipe 8: Parsing RNA 2D Structures in the Vienna Format Recipe 9: Parsing BLAST XML Output Recipe 10: Parsing SBML Files  Recipe 11: Running BLAST  Recipe 12: Accessing, Downloading, and Reading Web Pages in Python  Recipe 13: Parsing HTML Files  Recipe 14: Split a PDB File into PDB Chain Files  Recipe 15: Find the Two Closest Calpha Atoms in a PDB Structure  Recipe 16: Extract the Interface between Two PDB Chains Recipe 17: Building Homology Models Using Modeller  Recipe 18: RNA 3D Homology Modeling with ModeRNA  Recipe 19: Calculating RNA Base Pairs from a 3D Structure  Recipe 20: A Real Case of Structural Superimposition: The Serine Protease Catalytic Triad  Appendix A: Command Overview Appendix B: Python Resources Appendix C: Record Samples Appendix D: Handling Directories and Programs with UNIX