cstag 0.1.1

Convert cstag format from short to long, vice versa

cstag

cstag is a Python module to manipulate minimap2's CS tag.

• cstag.shorten(): to convert a cs tag from long to short format
• cstag.lengthen(): to convert a cs tag from short to long format
• cstag.consensus(): to generate a consensus cs tag from multiple cs tags
• cstag.to_html(): to output html report

Installation

From PyPI:

pip install cstag

Examples

Shorten/Lengthen

import cstag

"""
Convert long format of cs tag into short format
"""
cs = "cs:Z:=ACGT*ag=CGT"
cstag.shorten(cs)
# => cs:Z::4*ag:3


"""
Convert short format of cs tag into long format
"""
cs = "cs:Z::4*ag:3"
cigar = "8M"
seq = "ACGTACGT"
cstag.lengthen(cs, cigar, seq)
# => cs:Z:=ACGT*ag=CGT

Call consensus

import cstag
cs_list = ["cs:Z:=ACGT", "cs:Z:=AC*gt=T", "cs:Z:=C*gt=T", "cs:Z:=C*gt=T", "cs:Z:=ACT+ccc=T"]
cigar_list = ["4M", "4M", "1S3M", "3M", "3M3I1M"]
pos_list = [1, 1, 1, 2, 1]
cstag.consensus(cs_list, cigar_list, pos)
# => cs:Z:=AC*gt*T

Output HTML report

import cstag
cs = "cs:Z:=AC+GGG=T-ACGT*at~gt10cg=GNNN"
output = "report"
description = "Example"
cstag.to_html(cs, output, description)
# => Output "report.html"

The report.html is :point_down: