Converts a part of an alignment (.PAF perhaps others sometimes) to a Circos image using BED and fasta files.
- biopython
- circos
- pandas
- numpy
usage: p2c.py [-h] [--templates TEMPLATES] [--min-length MIN_LENGTH] [--bed BED] [--cov COV] [--snps SNPS] PAF Query Reference BED Output Circos plot all alignments against each target in the .paf file. positional arguments: PAF An alignment .paf formatted Query A fasta file containing the query sequences Reference A fasta file containing the target sequences BED A .bed file containing the target contigs regions to plot Output A directory path optional arguments: -h, --help show this help message and exit --templates TEMPLATES, -t TEMPLATES A directory path containing the template files --min-length MIN_LENGTH, -m MIN_LENGTH Minimum length. Default: 1000. --bed BED, -b BED A .bed file with regions to highlight. --scov COV, -sc COV A file formatted like the output of samtools depth. --ccov COV, -cc COV A file formatted for circos. --snps SNPS, -s SNPS A .vcf file of the query and/or target.