isotools 0.2.0.dev3

Framework for the analysis of long read transcriptome sequencing data

isotools

IsoTools is a python module for Long Read Transcriptome Sequencing (LRTS) analysis.

Key features:

• Import of LRTS bam files (aligned full length transcripts).
• Import of reference annotation in gff3/gtf format.
• Computation of quality control metrics.
• Annotation and classification of novel transcripts with biologically motivated classification scheme.
• Definition of alternative splicing events based on segment graphs.
• Detection of differential alternative splicing between samples and groups of samples.
• Data visualization.

documentation:

The documentation, including tutorials with real-world case studies and the complete API reference is available at readthedocs

installation:

Isotools is available from PyPI, and can be installed with the pip command:

python3 -m pip install isotools

Alternatively, to install from github, use the following command:

git clone https://github.com/MatthiasLienhard/isotools.git
cd isotools
python3 -m pip install .

usage:

This code block demonstrates the basic file import with isoseq. For a more comprehensive real world example see the tutorials.

from  isotools.transcriptome import Transcriptome
import logging
logging.basicConfig(format='%(levelname)s:%(message)s', level=logging.INFO)
isoseq=Transcriptome.from_reference('reference_file.gff3.gz')
isoseq_bam_fn={'sample1':'isoseq_fn_s1.bam', 'sample2':'isoseq_fn_s2.bam'}
groups={'sample1':'control', 'sample2':'treatment'}
for sa,bam in isoseq_bam_fn.items():
    isoseq.add_sample_from_bam(bam, sample_name=sa, group=groups[sa]) 
isoseq.add_biases('genome.fa')
isoseq.make_index()
isoseq.add_filter()
isoseq.save('example_isotools.pkl')

Citation and feedback:

• If you run into any issues, please use the github issues report feature.
• For general feedback, please write me an email to [e-mail].
• If you use isotools in your publication, please cite the following paper: IsoTools: IsoTools: a python toolbox for long-read transcriptome sequencing (in preparation)