Source

bx-python / setup.py

Author Commit Message Labels Comments Date
olgert denas
scripts for chain to EPO (.out) conversion and feature mapping
mruffalo
If Python 3, use 2to3 distutils builder instead
mruffalo
setup.py: correctly identify Python 3 as >= 2.4 for issue #35
James Taylor
BigWig/BigBed: fixed some missing type declerations in the summarization code (~20 times faster)
James Taylor
Merge to restore BGZFFile
James Taylor
Backed out changeset c1e165e97419, bgzf is still useful.
James Taylor
bigbed support
Kanwei Li
Bump to 0.7.0, fix doc URL
James Taylor
BigWigFile subclassing BBIFile, support for creating summaries from 'unzoomed' data points.
James Taylor
BBI Files: Summarization from zoom levels now working. Still need to implement summarization from full data (type specific) to have complete summary support.
James Taylor
Renaming cir_tree to cirtree_file to be consistent with other packages
James Taylor
First steps toward bigbed/bigwig reading -- working read-only implementations of bPlusTree and cirTree, bbiFile can find and parse summaries
James Taylor
Up version to 0.6.0, release to pypi
Kanwei Li
- Changes to array_tree to enable frequencies (how many times a node is visited, and also option to disable leaf nodes to save space - New api allows different readers to be used to create array_trees - New basic BED reader - Rename arrays/IntervalReader to arrays/WiggleReader - More tests for array_tree - Fix unit test for align/tools/thread - Fix typos
Kanwei Li
Remove bgzf as it's no longer planned to be used
James Taylor
BGZF support (really simple wrapper to code from samtools)
Kanwei Li
New ClusterTree that fixes a node merging problem in the original, and that uses less memory
James Taylor
Cythonized wiggle reader, added script for converting wiggle to array_tree.
James Taylor
Exclude test modules and privat modules (starting with _) from apidocs
James Taylor
Added sphinx documentation skelaton from Istvan Albert. Modified styles to match bx.mathcs.emory.edu. Added support for sphinx to setup.py. Created a shortcut build_docs to build both API and sphinc documentation.
James Taylor
ArrayTree for storing block-sparse array data with summaries
Brent Pedersen
cleanup in intersection, remove old code, micro optimization checking for is None, rather than bool fix spelling of my name. :-)
James Taylor
Patch from Istvan Albert <iua1@psu.edu> to fix some windows compilation issues in bitsets and to disable some modules that currently don't compile in windows.
James Taylor
Integrate Cython version of quicksect from Brent Pederson. This replaces the old intersection package with a much faster and more functional version. API compatibility should be maintained
Nate Coraor
Per James, make the build-time numpy dependency conditional (this is so people building for their own platforms need not have numpy).
James Taylor
Fix package data (for template.ps)
James Taylor
New motif/matrix classes. Includes a reader for TRANSFAC style databases (which can be easily extended), and position specific weight/frequency and scoring matrix code using numpy. Fast string scoring is provided through a Cython extension. This doesn't do everything the bx.pwm module does, but I think it is a little better organized, and includes more documentation and tests. It would be nice to see what we can move from bx.pwm into here.
James Taylor
Make Cython optional.
James Taylor
Require Cython (Pyrex evolved) to build.
James Taylor
Read only twoBit support. Not yet using the SeqFile interface because I'm not sure how to make it fit a file that can contain many sequences. We probably need a "SeqCollection" interface, with an implementation for this, fasta, and a "directory full of nib files".
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