cstag 0.6.0

Python module to manipulate the minimap2's CS tag

cstag

cstag is a Python library designed for handling and manipulating minimap2's CS tags.

🌟Features

• cstag.call(): Generate a CS tag
• cstag.shorten(): Convert a CS tag from long to short format
• cstag.lengthen(): Convert a CS tag from short to long format
• cstag.consensus(): Generate a consensus cs tag from multiple cs tags
• cstag.mask(): Mask low-quality bases in a CS tag
• cstag.split(): Split a CS tag
• cstag.revcomp(): Converts a CS tag into its reverse complement.
• cstag.to_vcf(): Output VCF
• cstag.to_html(): Output HTML

Visit the documentation for more details.

🛠 Installation

Using PyPI:

pip install cstag

Using Bioconda:

conda install -c bioconda cstag

💡Usage

Generate CS Tags

import cstag

cigar = "8M2D4M2I3N1M"
md = "2A5^AG7"
seq = "ACGTACGTACGTACG"

print(cstag.call(cigar, md, seq))
# :2*ag:5-ag:4+ac~nn3nn:1

cstag.call(cigar, md, seq, long=True)
#  =AC*ag=TACGT-ag=ACGT+ac~nn3nn=G

Shorten or Lengthen CS Tags

import cstag

# Convert a CS tag from long to short
cs = "=ACGT*ag=CGT"

cstag.shorten(cs)
#  :4*ag:3


# Convert a CS tag from short to long
cs = ":4*ag:3"
cigar = "8M"
seq = "ACGTACGT"

cstag.lengthen(cs, cigar, seq)
#  =ACGT*ag=CGT

Generate a Consensus

import cstag

cs_list = ["=ACGT", "=AC*gt=T", "=C*gt=T", "=C*gt=T", "=ACT+ccc=T"]
cigar_list = ["4M", "4M", "1S3M", "3M", "3M3I1M"]
pos_list = [1, 1, 1, 2, 1]

cstag.consensus(cs_list, cigar_list, pos_list)
#  =AC*gt*T

Mask Low-Quality Bases

import cstag

cs = "=ACGT*ac+gg-cc=T"
cigar = "5M2I2D1M"
qual = "AA!!!!AA"
phred_threshold = 10
cstag.mask(cs, cigar, qual, phred_threshold)
#  =ACNN*an+ng-cc=T

Split a CS Tag

import cstag

cs = "=ACGT*ac+gg-cc=T"
cstag.split(cs)
#  ['=ACGT', '*ac', '+gg', '-cc', '=T']

Reverse Complement of a CS Tag

import cstag

cs = "=ACGT*ac+gg-cc=T"
cstag.revcomp(cs)
#  =A-gg+cc*tg=ACGT

Generate VCF Report

import cstag
cs_tag = "=AC*gt=T-gg=C+tt=A"
chrom = "chr1"
pos = 1
print(cstag.to_vcf(cstag, chrom, pos))
"""
##fileformat=VCFv4.2
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
chr1	3	.	G	T	.	.	.
chr1	4	.	TGG	T	.	.	.
chr1	5	.	C	CTT	.	.	.
"""

Generate HTML Report

import cstag
from pathlib import Path

cs_tag = "=AC+GGG=T-ACGT*at~gt10cg=GNNN"
description = "Example"

cs_tag_html = cstag.to_html(cs_tag, description)
Path("report.html").write_text(cs_tag_html)
# Output "report.html"

The resulting report.html looks like this :point_down:

📣Feedback

For questions, bug reports, or any other inquiries, feel free to reach out!
Please use GitHub Issues for reporting.