ReAlignPro: realignment of promoter sequences by centralizing transcription start sites and exporting MAF/BED/figures.
Project description
ReAlignPro
ReAlignPro is a command-line toolkit for:
fa2maf: identify orthologous regions via LASTZ reciprocal-best hits, align sequences with MUSCLE, and export MAF/TSV outputs.maf2bed: extract target-shared, others-absent positions from a MAF/MAF.GZ and write BED3 intervals.tsv2fig: generate PDF sequence-table plots from a conservation-matrix TSV.
Installation
pip
pip install realignpro
Note: fa2maf requires external binaries available in PATH:
lastzmusclesamtools
conda (recommended)
mamba install -c conda-forge -c bioconda realignpro lastz muscle samtools
Quick start
realignpro --help
realignpro fa2maf --help
realignpro maf2bed --help
realignpro tsv2fig --help
License
GPL-3.0
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