دانلود کتاب Biopython Tutorial and Cookbook

فهرست مطالب :

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