BioNumPy documentation

Home

• BioNumPy at a glance
• Getting started with BioNumPy in 10 minutes
• Using BioNumPy in your existing project

Tutorials

• Filtering FASTQ reads
• Working with BAM-files
• Getting read pileup inside peaks (intervals)
• FastQC-like quality-checking of FASTQ files
• Computing GC content inside genes
• Position Weight Matrix
• Simulating sequence datasets
• Computing the similarity between two BED-files
• Extracting kmers around snps

Interoperability

• Numpy Interoperability
• Using BioNumPy with Biopython
• Pandas Interoperability

BioNumPy Concepts

• Reading files
  • Method 1: Reading all your data at once
  • Method 2: Reading a single chunk from a large file
  • Method 3: Reading whole file as a stream of chunks
• Encodings
  • Encoding data using a specific encoding
  • Supported encodings
  • When having already encoded data (advanced usage)
• Supported file formats
  • Example
• Reading a new file format
• Sequences
  • EncodedArray
  • EncodedRaggedArray
  • Absolute basics of EncodedRaggedArray
  • Reading sequences from file
  • Functions workin on sequences
• Intervals
  • Independent Operations
  • Operations with dependencies
  • Genomic Intervals
• Working with Multiple Files/Data Sources
  • Sort Order
  • Two Indexed Files
• Broadcastable Functions
  • Elementwise broadcasting in NumPy
  • Vectorwise broadcasting
  • Sequence broadcasting

API documentation

• BnpDataclass
  • API documentation
    • bnpdataclass()
    • replace()
    • make_dataclass()
• Genome arithmetics
  • API documentation
    • forbes()
    • jaccard()
    • sort_intervals()
    • merge_intervals()
    • get_pileup()
    • get_boolean_mask()
• Genomic Data
  • API documentation
    • Genome
    • GenomicArray
    • GenomicIntervals
    • GenomicLocation
    • GenomicAnnotation
    • GenomicSequence
• IO
  • API documentation
    • bnp_open()
    • open_indexed()
    • count_entries()
    • BedBuffer
    • VCFBuffer
    • FastQBuffer
    • TwoLineFastaBuffer
    • IndexedFasta
• Sequences
  • API documentation
    • get_kmers()
    • get_minimizers()
    • get_motif_scores()
    • count_encoded()
    • match_string()
    • PWM
• Streams
  • API documentation
    • streamable()

Other

• Developer guide
  • Getting started and how to contribute
  • Setting up your development environment
    • Step 1 (Optional): Install development version of npstructures
    • Step 2: Install BioNumPy locally (not from PyPi)
    • Step 3: Install development dependencies
    • Step 4: Test your installation
  • How we do testing in BioNumPy
    • Dependencies with NpStructures
  • Making examples
    • Overview
    • Testing of examples
    • Using data in your examples
  • Writing documentation
    • Structure of documentation
    • Writing code in the documentation
  • Design principles and code overview
    • Overview
    • Vectorized File I/O
    • @bnpdataclass
    • Utility Functions
    • Encodings
  • Implementing encodings
• BioNumPy manuscript
  • Abstract
  • Introduction
  • Results
    • The BioNumPy Library
    • Benchmarks
    • Example usage
      • Example 1: Using BioNumPy on sequence data
      • Example 2: Analysing motif matches inside transcription factor peaks
  • Implementation details
    • Data representation
    • Development
  • Discussion