Framework for the analysis of long read transcriptome sequencing data
Reason this release was yanked:
broken requirements (umap)
Project description
isotools
python module for isoseq postprocessing
documentation:
http://medips.molgen.mpg.de/isoseq/
installation:
Isotools is available from PyPI, and can be installed with the pip command:
python3 -m pip install isotools
To install from github:
git clone https://github.molgen.mpg.de/lienhard/isotools.git
cd isotools
python3 -m pip install .
usage:
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')
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