rwrap
A thin wrapper around rpy2 with strong opinions on how data types should be converted. This enables easy usage of R packages from Python with no boilerplate code.
Warning: still work-in-progress, issues and PRs welcome
Installation
pip install rwrapUsage
For example, accessing biomaRt can be as simple as follows:
from rwrap import biomaRt
snp_list = ['rs7329174', 'rs4948523', 'rs479445']
ensembl = biomaRt.useMart('ENSEMBL_MART_SNP', dataset='hsapiens_snp')
df = biomaRt.getBM(
attributes=['refsnp_id', 'chr_name', 'chrom_start', 'consequence_type_tv'],
filters='snp_filter', values=snp_list, mart=ensembl
)
print(df) # pandas.DataFrame
# refsnp_id chr_name chrom_start consequence_type_tv
# 1 rs479445 1 60875960 intron_variant
# 2 rs479445 1 60875960 NMD_transcript_variant
# 3 rs4948523 10 58579338 intron_variant
# 4 rs7329174 13 40983974 intron_variantCheck the tests/ directory for more examples showing how to rewrite R scripts in Python.
Tests
A comprehensive test suite aims at providing stability and avoiding regressions.
The examples in tests/ are validated using pytest.
Run tests as follows:
$ pytest tests/
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