pyseqlib 0.3.0

pySeqLib: A small python library to process sequencing data.

A small python library to process sequencing data. It is under active development.

What’s inside?

• intronX: a program to fetch sequence related features for introns: 1) length, 2) splice site motif strength, 3) second structure energy 4) frequecy of k-mers. See manual and example.

• pymfold: a python wrap of mfold for calculate energy of RNA secondary structure. We got installation issue from mfold, similar as this. Therefore, we recommend using pyRNAfold instead.

• pyRNAfold: a python wrap of for another predictor, RNAfold, of RNA secondary structure energy. It is from the ViennaRNA package, which can be installed from the source code, or from BioConda.

• motif-score: a motif score calculate

• a sequence mapper to find lariat in RNA-seq reads (under test)

• a sam file resampling method

How to install?

Pyseqlib was initially developed in Python 2 environment, hence best to be used in Py2 environment. By using Anaconda platform, no matter Py2 or Py 3, it is easy to set up a conda environment with Py2, for example by following commond:

conda create -n Py2 python=2.7 numpy==1.15.4 pysam==0.15.2 Cython==0.29.3 matplotlib==2.2.3
source activate Py2

Once you are in a Python 2 environment, you can download the codes from this github repository and then run the following command line:

python setup.py install

Or

pip install -U git+https://github.com/huangyh09/pyseqlib

If you don’t have the root permission, add --user.

Rquired libraries: pysam, numpy, Cython.