Python utility for understanding whole genome bisulfite data and viewing it as a whole
Project description
Mehtrandir
Installation
This package is available on anaconda and can be installer with the following command
conda install -c skanderpoit methrandir
Usage
Directly from the command line:
usage: methrandir.py [-h] -f FILES [-o OUT_PREFIX] [-outdir OUTDIR] [-m METHOD] [-c MIN_COVERAGE] [-C CONTEXTS [CONTEXTS ...]] [-F FORCE] [-p P_VALUE]
Methylation Data Overview Utility
optional arguments:
-h, --help show this help message and exit
-f FILES, --files FILES
tab seperated file containing paths of sorted bismark CX reports and their
-o OUT_PREFIX, --out_prefix OUT_PREFIX
output files prefix
-outdir OUTDIR, --outdir OUTDIR
output directory
-m METHOD, --method METHOD
model biological replicates : weighted_average | anova
-c MIN_COVERAGE, --min_coverage MIN_COVERAGE
minimum number of reads for each position on all samples
-C CONTEXTS [CONTEXTS ...], --contexts CONTEXTS [CONTEXTS ...]
list of contexts to be considered for downstream analysis : CG,CHG,CHH
-F FORCE, --force FORCE
Force recreation of filtered files
-p P_VALUE, --p_value P_VALUE
p_value for statistical tests
Or imported as a module in your python scri
from methrandir import methrandir
methrandir.readlines() needs a .tsv
file describing raw data(Sorted Bismark CX reports) and can take other arguments to further filter data for each position.
methrandir.compute_pca() takes in the product of readfiles and applies pca and generates some graphs.
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
methrandir-0.0.4.tar.gz
(7.0 MB
view hashes)
Built Distribution
Close
Hashes for methrandir-0.0.4-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 447b65316403bdd982f6433986d0d089eebd46fcbdab4cecd87ea839a9b4c721 |
|
MD5 | c326d95a7a2e59f88ff00e01b539998f |
|
BLAKE2b-256 | f074fde5875abfe95f06e6d664dd6a7de6d1091ba8807589c518429777cd3b39 |