Skip to main content

Python Package for RNA structurome quantification analysis.

Project description

CONTENTS AND COPYRIGHT

This package is used for maniputating genome annotation and seqeunce files, such as Bed, GenePred, BAM, Wiggle and BigWig formats. Users interested in this package should contact yfwang0405@gmail.com for details. This package uses the Vienna RNA Package lib and H directories (external/RNAlib/fold) and RNAStructure libs (external/RNAlib/plot), and users should read the COPYING or ReadMe.txt files inside and behave accordingly. All files are copyrighted, but license is hereby granted for personal, academic and non-profit use. Commercial users should contact yfwang0405@gmail.com.

MANUALS

http://rsqwiki.appspot.com

SOURCES CODES

https://pypi.python.org/pypi/rsq

PREREQUISITES

1. python 2.7, python-dev
2. numpy >= 1.4.1 (automatically installed)
3. ngslib >= 1.1.10 for NGS data processing (automatically installed)
4. fisher >= 0.1.4 for fisher exact test ((automatically installed)
4. sfold 2.2 stand-alone executable (http://sfold.wadsworth.org/License_info.html)

GENERAL INSTALL INSTRUCTIONS

1. Install from Python Package Index (https://pypi.python.org)
> easy_install --prefix=$HOME/local rsq

2. Install from source file (including the demo example files)
>easy_install --editable --build-directory package_source/ rsq
>cd package_source
>python setup.py install --prefix=install_path

3. sfold 2.2
Download the stand-alone executable from http://sfold.wadsworth.org/License_info.html
Run configure file
>cd SFOLD2.2_HOME
>./configure
Test sfold in command line before use:
>bin/sfold
If successful, add sfold binary file to system PATH by:
PATH=$PATH:SFOLD2.2_HOME/bin/
export PATH

MAJOR MODULES

- Data formats:
FastD, FastC, FastS and EFastS to represent data used in RSQ.

- IO:
Readers for each data format

- Predictor:
Wrappers of a series of RNA secondary structure prediction tools.
RNAfold, mfold, UNAFold, sfold, et. al.
Note: make sure the command/program is callable in shell before call it in RSQ.

- Algorithm:
EM algoritm, Boltzmann sampling, structure distance calculation, et. al.

- Utils:
Utilites. Temperature conversion, structure format conversion, et. al.

- ThreadSafeFile:
Used in threading processing procedures.

EXAMPLES

Examples are in the examples folder.
1. Dealing with genes without isoforms.
2. Dealing with genes with multiple isoforms.
3. Advanced usage in tuning parameters and adding in external input.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

rsq-2.0.2.tar.gz (594.7 kB view details)

Uploaded Source

File details

Details for the file rsq-2.0.2.tar.gz.

File metadata

  • Download URL: rsq-2.0.2.tar.gz
  • Upload date:
  • Size: 594.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No

File hashes

Hashes for rsq-2.0.2.tar.gz
Algorithm Hash digest
SHA256 cdcb2119c40638ee0f5bf5e5a9db1af1f4b16464f2174e061a4984ec257c5ea3
MD5 77bdd99dc11eeaf9f71b8deaadf4b170
BLAKE2b-256 b46f8f9ac59f1c776805bf82f0b639b67a25fb794c6aeef3fe2796cd0a6cec84

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page