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[](https://pypi.org/project/cstag/)
[](https://pypi.org/project/cstag/)
[](https://anaconda.org/bioconda/cstag)
# cstag
`cstag` is a Python module to manipulate [minimap2's CS tag](https://github.com/lh3/minimap2#cs).
- `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.mask()`: to mask low-quality bases in a cs tag
- `cstag.to_html()`: to output html report
<!-- - `cstag.to_mids()`: to convert cs tag into [compressed MIDS format](https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001507#:~:text=S6%20Fig.%20Compressed%20MIDS%20conversion.) (under-development:construction_worker:) -->
See [documentation](https://akikuno.github.io/cstag/cstag/) for more information.
## Installation
From [PyPI](https://pypi.org/project/cstag/):
```bash
pip install cstag
```
From [Bioconda](https://anaconda.org/bioconda/cstag):
```bash
conda install -c bioconda cstag
```
## Examples
### Shorten/Lengthen
```python
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
```python
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
```python
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
```
### Output HTML report
```python
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:
<img width="414" alt="example_report" src="https://user-images.githubusercontent.com/15861316/158910398-67f480d2-8742-412a-b528-40e545c46513.png">
