Biopython Tutorial and Cookbook

Introduction
	What is Biopython?
	What can I find in the Biopython package
	Installing Biopython
	Frequently Asked Questions (FAQ)
Quick Start – What can you do with Biopython?
	General overview of what Biopython provides
	Working with sequences
	A usage example
	Parsing sequence file formats
		Simple FASTA parsing example
		Simple GenBank parsing example
		I love parsing – please don't stop talking about it!
	Connecting with biological databases
	What to do next
Sequence objects
	Sequences and Alphabets
	Sequences act like strings
	Slicing a sequence
	Turning Seq objects into strings
	Concatenating or adding sequences
	Changing case
	Nucleotide sequences and (reverse) complements
	Transcription
	Translation
	Translation Tables
	Comparing Seq objects
	MutableSeq objects
	UnknownSeq objects
	Working with strings directly
Sequence annotation objects
	The SeqRecord object
	Creating a SeqRecord
		SeqRecord objects from scratch
		SeqRecord objects from FASTA files
		SeqRecord objects from GenBank files
	Feature, location and position objects
		SeqFeature objects
		Positions and locations
		Sequence described by a feature or location
	Comparison
	References
	The format method
	Slicing a SeqRecord
	Adding SeqRecord objects
	Reverse-complementing SeqRecord objects
Sequence Input/Output
	Parsing or Reading Sequences
		Reading Sequence Files
		Iterating over the records in a sequence file
		Getting a list of the records in a sequence file
		Extracting data
	Parsing sequences from compressed files
	Parsing sequences from the net
		Parsing GenBank records from the net
		Parsing SwissProt sequences from the net
	Sequence files as Dictionaries
		Sequence files as Dictionaries – In memory
		Sequence files as Dictionaries – Indexed files
		Sequence files as Dictionaries – Database indexed files
		Indexing compressed files
		Discussion
	Writing Sequence Files
		Round trips
		Converting between sequence file formats
		Converting a file of sequences to their reverse complements
		Getting your SeqRecord objects as formatted strings
	Low level FASTA and FASTQ parsers
Multiple Sequence Alignment objects
	Parsing or Reading Sequence Alignments
		Single Alignments
		Multiple Alignments
		Ambiguous Alignments
	Writing Alignments
		Converting between sequence alignment file formats
		Getting your alignment objects as formatted strings
	Manipulating Alignments
		Slicing alignments
		Alignments as arrays
	Alignment Tools
		ClustalW
		MUSCLE
		MUSCLE using stdout
		MUSCLE using stdin and stdout
		EMBOSS needle and water
		Biopython's pairwise2
	Pairwise sequence alignment
		Basic usage
		The pairwise aligner object
		Match and mismatch scores
		Affine gap scores
		General gap scores
		Iterating over alignments
		Alignment objects
		Example
BLAST
	Running BLAST over the Internet
	Running BLAST locally
		Introduction
		Standalone NCBI BLAST+
		Other versions of BLAST
	Parsing BLAST output
	The BLAST record class
	Dealing with PSI-BLAST
	Dealing with RPS-BLAST
BLAST and other sequence search tools
	The SearchIO object model
		QueryResult
		Hit
		HSP
		HSPFragment
	A note about standards and conventions
	Reading search output files
	Dealing with large search output files with indexing
	Writing and converting search output files
Accessing NCBI's Entrez databases
	Entrez Guidelines
	EInfo: Obtaining information about the Entrez databases
	ESearch: Searching the Entrez databases
	EPost: Uploading a list of identifiers
	ESummary: Retrieving summaries from primary IDs
	EFetch: Downloading full records from Entrez
	ELink: Searching for related items in NCBI Entrez
	EGQuery: Global Query - counts for search terms
	ESpell: Obtaining spelling suggestions
	Parsing huge Entrez XML files
	HTML escape characters
	Handling errors
	Specialized parsers
		Parsing Medline records
		Parsing GEO records
		Parsing UniGene records
	Using a proxy
	Examples
		PubMed and Medline
		Searching, downloading, and parsing Entrez Nucleotide records
		Searching, downloading, and parsing GenBank records
		Finding the lineage of an organism
	Using the history and WebEnv
		Searching for and downloading sequences using the history
		Searching for and downloading abstracts using the history
		Searching for citations
Swiss-Prot and ExPASy
	Parsing Swiss-Prot files
		Parsing Swiss-Prot records
		Parsing the Swiss-Prot keyword and category list
	Parsing Prosite records
	Parsing Prosite documentation records
	Parsing Enzyme records
	Accessing the ExPASy server
		Retrieving a Swiss-Prot record
		Searching Swiss-Prot
		Retrieving Prosite and Prosite documentation records
	Scanning the Prosite database
Going 3D: The PDB module
	Reading and writing crystal structure files
		Reading a PDB file
		Reading an mmCIF file
		Reading files in the MMTF format
		Reading files in the PDB XML format
		Writing PDB files
		Writing mmCIF files
	Structure representation
		Structure
		Model
		Chain
		Residue
		Atom
		Extracting a specific Atom/Residue/Chain/Model from a Structure
	Disorder
		General approach
		Disordered atoms
		Disordered residues
	Hetero residues
		Associated problems
		Water residues
		Other hetero residues
	Navigating through a Structure object
	Analyzing structures
		Measuring distances
		Measuring angles
		Measuring torsion angles
		Determining atom-atom contacts
		Superimposing two structures
		Mapping the residues of two related structures onto each other
		Calculating the Half Sphere Exposure
		Determining the secondary structure
		Calculating the residue depth
	Common problems in PDB files
		Examples
		Automatic correction
		Fatal errors
	Accessing the Protein Data Bank
		Downloading structures from the Protein Data Bank
		Downloading the entire PDB
		Keeping a local copy of the PDB up to date
	General questions
		How well tested is Bio.PDB?
		How fast is it?
		Is there support for molecular graphics?
		Who's using Bio.PDB?
Bio.PopGen: Population genetics
	GenePop
Phylogenetics with Bio.Phylo
	Demo: What's in a Tree?
		Coloring branches within a tree
	I/O functions
	View and export trees
	Using Tree and Clade objects
		Search and traversal methods
		Information methods
		Modification methods
		Features of PhyloXML trees
	Running external applications
	PAML integration
	Future plans
Sequence motif analysis using Bio.motifs
	Motif objects
		Creating a motif from instances
		Creating a sequence logo
	Reading motifs
		JASPAR
		MEME
		TRANSFAC
	Writing motifs
	Position-Weight Matrices
	Position-Specific Scoring Matrices
	Searching for instances
		Searching for exact matches
		Searching for matches using the PSSM score
		Selecting a score threshold
	Each motif object has an associated Position-Specific Scoring Matrix
	Comparing motifs
	De novo motif finding
		MEME
	Useful links
Cluster analysis
	Distance functions
	Calculating cluster properties
	Partitioning algorithms
	Hierarchical clustering
	Self-Organizing Maps
	Principal Component Analysis
	Handling Cluster/TreeView-type files
	Example calculation
Supervised learning methods
	The Logistic Regression Model
		Background and Purpose
		Training the logistic regression model
		Using the logistic regression model for classification
		Logistic Regression, Linear Discriminant Analysis, and Support Vector Machines
	k-Nearest Neighbors
		Background and purpose
		Initializing a k-nearest neighbors model
		Using a k-nearest neighbors model for classification
	Naïve Bayes
	Maximum Entropy
	Markov Models
Graphics including GenomeDiagram
	GenomeDiagram
		Introduction
		Diagrams, tracks, feature-sets and features
		A top down example
		A bottom up example
		Features without a SeqFeature
		Feature captions
		Feature sigils
		Arrow sigils
		A nice example
		Multiple tracks
		Cross-Links between tracks
		Further options
		Converting old code
	Chromosomes
		Simple Chromosomes
		Annotated Chromosomes
KEGG
	Parsing KEGG records
	Querying the KEGG API
Bio.phenotype: analyse phenotypic data
	Phenotype Microarrays
		Parsing Phenotype Microarray data
		Manipulating Phenotype Microarray data
		Writing Phenotype Microarray data
Cookbook – Cool things to do with it
	Working with sequence files
		Filtering a sequence file
		Producing randomised genomes
		Translating a FASTA file of CDS entries
		Making the sequences in a FASTA file upper case
		Sorting a sequence file
		Simple quality filtering for FASTQ files
		Trimming off primer sequences
		Trimming off adaptor sequences
		Converting FASTQ files
		Converting FASTA and QUAL files into FASTQ files
		Indexing a FASTQ file
		Converting SFF files
		Identifying open reading frames
	Sequence parsing plus simple plots
		Histogram of sequence lengths
		Plot of sequence GC%
		Nucleotide dot plots
		Plotting the quality scores of sequencing read data
	Dealing with alignments
		Calculating summary information
		Calculating a quick consensus sequence
		Position Specific Score Matrices
		Information Content
	Substitution Matrices
		Using common substitution matrices
		Creating your own substitution matrix from an alignment
	BioSQL – storing sequences in a relational database
The Biopython testing framework
	Running the tests
		Running the tests using Tox
	Writing tests
		Writing a print-and-compare test
		Writing a unittest-based test
	Writing doctests
	Writing doctests in the Tutorial
Advanced
	Parser Design
	Substitution Matrices
		SubsMat
		FreqTable
Where to go from here – contributing to Biopython
	Bug Reports + Feature Requests
	Mailing lists and helping newcomers
	Contributing Documentation
	Contributing cookbook examples
	Maintaining a distribution for a platform
	Contributing Unit Tests
	Contributing Code
Appendix: Useful stuff about Python
	What the heck is a handle?
		Creating a handle from a string