Modules

Contents:

Genomics

• AString.py - a compact string of characters
• FastaIterator.py - iterate over fasta files
• Intervals.py -
• Mali.py - Tools for multiple alignments
• MaliIO.py -
• GenomicIO.py - Subroutines for working on I/O of large genomic files
• Maq.py -
• AGP.py - working with AGP files
• Regions.py - helper functions for working with genomic segments
• ProfileLibrary.py -
• ProfileLibraryCompass.py -

Phylogeny

• PamMatrices.py -

Parsers and wrappers

• WrapperAdaptiveCAI.py -
• WrapperBl2Seq.py -
• WrapperENC.py -
• WrapperMuscle.py -

Math and Stats

• CorrespondenceAnalysis.py -
• Histogram.py - Various functions to deal with histograms
• Histogram2D.py - functions for handling two-dimensional histograms.
• MatlabTools.py -

Gpipe and OPTIC

• Exons.py - A library to read/write/manage exons.
• Orthologs.py - tools to deal with Leo’s orthology pipeline.
• BlastAlignments.py - tools for working with alignments

Tools

• Experiment.py - Tools for scripts
• CSV.py - Tools for parsing CSV files
• IOTools - tools for I/O operations
• Iterators.py - general purpose iterators.
• Database.py -
• ExternalList.py - large disk-based lists
• ProgressBar.py -

Pipelines

• PipelineTracks.py - Definition of tracks in pipelines
• PipelineTracks.py - Definition of tracks in pipelines

Plotting

modules/GDLDraw.rst

Other

• RLE.py - a simple run length encoder
• SVGdraw.py - generate SVG drawings
• SetTools.py - Tools for working on sets
  • Code
• Sockets.py - working with sockets
• GraphTools.py -
  • Code
• Cluster.py - module for running a job in parallel on the cluster

Obsolete

• Intervalls.py -
  • Code
• IntervallsWeigted.py - working with weigted intervals
• SaryFasta.py - index fasta files by suffix array
• Fasta.py - Methods for dealing with fasta files.
• SuffixArray.py - sarry frontend
  • Code

Unsorted

Modules not sorted into categories.

• BlatTest.py -
  • Code
• CBioPortal.py - Interface with the Sloan-Kettering cBioPortal webservice
• CSV2DB.py - utilities for uploading a table to database
  • Purpose
  • Usage
  • Documentation
  • Code
• GDLDraw.py -
  • Code
• Glam2.py - Parser for MAST files.
• Glam2Scan.py - Parser for MAST files
• IGV.py - Simple wrapper to the IGV socket interface
• Logfile.py - logfile parsing
  • Purpose
  • Usage
  • Documentation
  • Code
• MAST.py - Parser for MAST files
• Tophat.py - working with tophat/cufflinks output files
  • Code
• VCF.py - Tools for working with VCF files
  • Code
• MACS.py - Parser for MACS output
  • API
• WrapperZinba.py - utility functions for zinba output
  • Purpose
  • Usage
  • Documentation
  • Code