Manipulating biological data

Sequences and Alignments

• Loading a sequence from a file
• Loading an alignment from a file or url
  • Loading aligned sequences
  • Loading unaligned sequences
  • Loading from a url
  • Specifying the file format
• Specifying the sequence molecular type
• Making an alignment from standard python objects
  • From a dict of strings
  • From a series of strings
  • Stripping label characters on loading
• Making a sequence collection from standard python objects
• Loading sequences using format parsers
  • Loading FASTA sequences from an open file or list of lines
  • Handling overloaded FASTA sequence labels
• Sequences
  • Generic molecular types
  • DNA and RNA sequences
• Protein sequences
  • Creating a ProteinSequence with a name
  • Converting a DNA sequence string to protein sequence string
  • Converting a nucleic acid sequence object to protein
  • Loading protein sequences from a Phylip file
• Sequence Collections and Alignments
  • What’s the difference between Alignment and ArrayAlignment?
  • Basic Collection objects
  • Adding new sequences to an existing collection or alignment
  • The elements of a collection or alignment
  • Alignments
  • Slicing an alignment
  • Computing alignment statistics
• Features
  • How to create a custom Feature
  • How to load bulk Features from a File
  • How to query a Sequence or Alignment for Features
  • Examples using the methods available on Features
• Annotation Databases
  • What are the different types of AnnotationDb?
  • How to create a standalone BasicAnnotationDb
  • How to load an standalone AnnotationDb from a data file
  • How to generate a summary of an AnnotationDb
  • How to add custom features to an AnnotationDb
  • How to write an AnnotationDb to disk for efficient re-loading
  • How to query an AnnotationDb
  • How to interrogate an AnnotationDb
  • How to combine two AnnotationDb instances
  • How to assign an AnnotationDb to a sequence
• Molecular types
  • Available molecular types
  • Getting a MolType
  • Using a MolType to get ambiguity codes
  • MolType definition of degenerate codes
  • Nucleic acid MolType and complementing
  • Making sequences
  • Verify sequences
  • Making a custom MolType
• Alphabets
  • Alphabet and MolType
  • Creating tuple alphabets
  • Convert a sequence into integers
  • Convert integers to a sequence

Genetic code

• Available genetic codes
• Using genetic codes

Trees

• Trees