Convert SAM alignments (± CpG methylation) into RGBA images.
Project description
omicimage
Convert sequencing alignments (SAM) — with optional CpG methylation reports — into RGBA images.
Installation
pip install omicimage
Command-line usage
Without methylation:
build-rgba-nomethylation sam_file.sam output_prefix [--width N] [--full-read] [--mapq N]
With methylation:
build-rgba-methylation sam_file.sam cpg_report.txt output_prefix [--width N] [--full-read] [--mapq N]
Output
Creates a timestamped folder containing:
image.png— RGBA representation of the datareadalignmentcoordinates.tsv— per-pixel genomic metadatametadata— image dimensions
Requirements
- Python 3.9+
- numpy, pillow, pysam, tqdm
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