From 9abf3ef3c3b91d17803fc3dd142e738da98917f9 Mon Sep 17 00:00:00 2001 From: Matt Holt Date: Tue, 22 Mar 2016 11:47:47 -0400 Subject: [PATCH] releasing a new version to pypi --- MUS/util.py | 2 +- README | 11 +++++++++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/MUS/util.py b/MUS/util.py index 63566ed..6d3e9f8 100644 --- a/MUS/util.py +++ b/MUS/util.py @@ -11,7 +11,7 @@ #I see no need for the versions to be different as of now DESC = "A multi-string BWT package for DNA and RNA." -VERSION = '0.2.8' +VERSION = '0.2.9' PKG_VERSION = VERSION validCharacters = set(['$', 'A', 'C', 'G', 'N', 'T']) diff --git a/README b/README index 6687c9f..553aa1b 100644 --- a/README +++ b/README @@ -1,7 +1,7 @@ Introduction ============ -Msbwt is a package for combining strings from sequencing into a data structure known as the multi-string BWT (MSBWT). +MSBWT is a package for combining strings from sequencing into a data structure known as the multi-string BWT (MSBWT). This structure allows for querying a k-mer in O(k) time regardless of how many strings are present in the MSBWT. This particular package was created originally for merging MSBWTs after creation. In short, this allows for multiple data sets to be combined into a single structure which allows for queries over both data sets simultaneously. @@ -48,6 +48,12 @@ Standard Library since Python 2.7. Its latest package can be downloaded from: http://code.google.com/p/argparse/ +*[numpy] - Tested with numpy 1.10.1 + +The numpy module provide various fast numerical functions for Python. Its latest package can be downloaded from: + + http://www.numpy.org + Installation ============ @@ -147,6 +153,7 @@ list of each along with the expected output. FM-index will need to be reconstructed for the new data format. decompress This function takes a compressed MSBWT and converts it back into its original uncompressed format. The auxiliary FM-index will need to be reconstructed for this format. + convert This function converted a raw text input BWT to our run-length encoded version. The latest release also includes installation of the Cython library used to load the MSBWTs and perform merges. After installation, the libraries are available through regular Python imports like so: @@ -155,4 +162,4 @@ installation, the libraries are available through regular Python imports like so msbwt = MultiStringBWT.loadBWT('/path/to/directory') msbwt.countOccurrencesOfSeq('CAT') -Other commands are available as well. For more information, refer to the code available at https://code.google.com/p/msbwt/. \ No newline at end of file +Other commands are available as well. For more information, refer to the code available at https://github.com/holtjma/msbwt. \ No newline at end of file