cstag 0.4.3

Python module to manipulate the minimap2's CS tag

cstag

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

• 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_html(): Output html report

See documentation for more information.

Installation

From PyPI:

pip install cstag

From Bioconda:

conda install -c bioconda cstag

Examples

Generate the cs tag

import cstag

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

cstag.call(cigar, md, seq, is_short_form=True)
# => cs:Z::2*ag:5-ag:4+ac~nn3nn:1

cstag.call(cigar, md, seq, is_short_form=False)
# => cs:Z:=AC*ag=TACGT-ag=ACGT+ac~nn3nn=G

Shorten/Lengthen

import cstag

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

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


# Convert a cs tag from short to long
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_list)
# => cs:Z:=AC*gt*T

Mask low-quality bases in a cs tag

import cstag

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

Split a cs tag

import cstag

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

Converts a cs tag into its reverse complement

import cstag

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

Output HTML report

import cstag
from pathlib import Path

cs = "cs:Z:=AC+GGG=T-ACGT*at~gt10cg=GNNN"
description = "Example"

cstag_html = cstag.to_html(cs, description)
Path("report.html").write_text(cstag_html)
# => Output "report.html"

The report.html is :point_down: