Analysis of allele-specific methylation in bisulfite DNA sequencing.
Project description
pyllelic
⭐ the project to show your appreciation. :arrow_upper_right:
pyllelic: a tool for detection of allelic-specific methylation variation in bisulfite DNA sequencing files.
Pyllelic documention is available at https://paradoxdruid.github.io/pyllelic/ and see pyllelic_notebook.ipynb
for an interactive demonstration.
Example exploratory use in jupyter notebook
Click to expand...
import pyllelic
pyllelic.set_up_env_variables( # Specify file and directory locations
base_path="/Users/abonham/documents/test_allelic/",
prom_file="TERT-promoter-genomic-sequence.txt",
prom_start="1293000",
prom_end="1296000",
chrom="5",
)
files_set = pyllelic.make_list_of_bam_files() # finds bam files
# Run pyllelic; make take some time depending on number of bam files
data = pyllelic.GenomicPositionData(config=pyllelic.config, files_set=files_set)
positions = data.positions
cell_types = data.cell_types
means_df = data.means
modes_df = data.modes
diff_df = data.diffs
individual_data = data.individual_data
data.save() # save methylation results
data.write_means_modes_diffs(filename="output.xlsx") # write output data to excel files
data.histogram("CELL_LINE", "POSITION") # visualize data for a point
data.quma_results["CELL_LINE"] # see summary data for a cell line
Dependencies and Installation
Conda environment
- Create a new conda environment using python 3.7:
conda create --name PYLLELIC python=3.7
conda activate PYLLELIC
Install pyllelic
pip install pyllelic
or
git clone https://github.com/Paradoxdruid/pyllelic.git
Authors
This software is developed as academic software by Dr. Andrew J. Bonham at the Metropolitan State University of Denver. It is licensed under the GPL v3.0.
This software incorporates implementation from QUMA, licensed under the GPL v3.0.
Project details
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