Modules

This section documents the modules used in CGAT scripts.

CGAT generic toolboxes

These are the modules that every script or module should use.

Genomics

File formats

Modules for parsing and working for data in specific formats.

• AGP.py - working with AGP files
• Bed.py - Tools for working with bed files
• Blat.py - tools for working with PSL formatted files and data
• CBioPortal.py - Interface with the Sloan-Kettering cBioPortal webservice
• FastaIterator.py - Iteration over fasta files
• Fastq.py - methods for dealing with fastq files
• GFF3 - Classes, functions and iterators for working with GFF3 files
• GTF.py - Classes and methods for dealing with GTF/GFF formatted files
• IndexedFasta.py - fast random access in fasta files
• IndexedGenome.py - Random access to interval lists
• Sra.py - Methods for dealing with short read archive files
• VCF.py - Tools for working with VCF files

Algorithms

• AString.py - strings as arrays of characters
• Genomics.py - Tools for working with genomic data
• Intervals.py - Utility functions for working with intervals
• Motifs.py -
• SequencePairProperties.py - Computing metrics for aligned sequences
• SequenceProperties.py - Computing metrics of nucleotide sequences
• Variants.py -

Wrappers

These modules wrap tools and provide routines for parsing their output.

• WrapperCodeML.py -
• IGV.py - Simple wrapper to the IGV socket interface
• Masker.py - Wrapper for sequence masking tools

Data processing

Math and Stats

• Histogram.py - Various functions to deal with histograms
• Histogram2D.py - functions for handling two-dimensional histograms.
• Stats.py - statistical utility functions
• MatrixTools.py -

Toolboxes

Toolboxes for generic problems.

• Iterators.py - Iterator functions
• SetTools.py - Tools for working on sets
• Tree.py - A phylogenetic tree
• TreeTools.py - Tools for working with trees

CGAT infrastructure

Below is a list of modules that are involved in maintainig the CGAT infrastructure such as logging, dependency tracking, etc.

Other

• RLE.py - a simple run length encoder
• SVGdraw.py - generate SVG drawings
• RateEstimation.py - utilities for computing rate estimates for codon models.

Unsorted

Modules not sorted into categories.