https://github.com/tseemann/cgmlst-dists
🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
https://github.com/tseemann/cgmlst-dists
cgmlst distance-matrix wgmlst
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🐻⇔🐨 Calculate distance matrix from ChewBBACA cgMLST allele call tables
- Host: GitHub
- URL: https://github.com/tseemann/cgmlst-dists
- Owner: tseemann
- License: gpl-3.0
- Created: 2020-03-02T04:19:36.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2023-09-26T12:08:07.000Z (over 1 year ago)
- Last Synced: 2024-06-13T00:03:07.604Z (12 months ago)
- Topics: cgmlst, distance-matrix, wgmlst
- Language: C
- Homepage:
- Size: 237 KB
- Stars: 24
- Watchers: 5
- Forks: 6
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
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[](https://www.gnu.org/licenses/gpl-3.0)
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# cgmlst-dists
Calculate distance matrix from
cgMLST allele call tables of ChewBBACA
## Quick Start
```
% cat test/boring.tab
FILE G1 G2 G3 G4 G5 G6
S1 1 INF-2 3 2 1 5
S2 1 1 1 1 NIPH 5
S3 1 2 3 4 1 3
S4 1 LNF 2 4 1 3
S5 1 2 ASM 2 1 3
S6 2 INF-8 3 PLOT3 PLOT5 3
% cgmlst-dists test/boring.tab > distances.tab
This is cgmlst-dists 0.4.0
Loaded 6 samples x 6 allele calls
Calulating distances... 100.00%
Done.
% cat distances.tab
S1 S2 S3 S4 S5
S1 0 3 2 3 1
S2 3 0 4 3 3
S3 2 4 0 1 1
S4 3 3 1 0 1
S5 1 3 1 1 0
S6 3 4 2 2 2
```
Any allelle calls that are not positive integers are converted to zero.
The distance is the
[hamming distance](https://en.wikipedia.org/wiki/Hamming_distance)
but with zeroes excluded.
It works by replacing any alphabet characters,
and the strings `PLOT5` and `PLOT3` with spaces.
It then converts the remaining tab separated
values to integers and ignoring negative signs.
Anything weird is set to zero.
## Installation
`cgmlst-dists` is written in C and has no other dependencies.
### Homebrew
```
brew install brewsci/bio/cgmlst-dists # COMING IN NOV 2020
```
### Bioconda
```
conda install -c bioconda cgmlst-dists
```
### Source
```
git clone https://github.com/tseemann/cgmlst-dists.git
cd cgmlst-dists
make
# run tests
make check
# optionally install to a specific location (default: /usr/local)
make PREFIX=/usr/local install
```
## Options
### `cgmlst-dists -h` (help)
```
SYNOPSIS
Pairwise CG-MLST distance matrix from allele call tables
USAGE
cgmlst-dists [options] chewbbaca.tab > distances.tsv
OPTIONS
-h Show this help
-v Print version and exit
-q Quiet mode; do not print progress information
-c Use comma instead of tab in output
-m N Output: 1=lower-tri 2=upper-tri 3=full [3]
-x N Stop calculating beyond this distance [9999]
URL
https://github.com/tseemann/cgmlst-dists
```
### `cgmlst-dists -v` (version)
Prints the name and version separated by a space in standard Unix fashion.
```
cgmlst-dists 0.4.0
```
### `cgmlst-dists -q` (quiet mode)
Don't print informational messages, only errors.
### `cgmlst-dists -c` (CSV mode)
Use a comma instead of a tab in the output table.
### `cgmlst-dists -m N` (output matrix format)
The output matrix is diagonal symmetric because _dist(A,B)=dist(B,A)_.
This means we only calculate half the matrix and mirror it.
You can choose to output the lower triangle, upper triangle, or both:
* `-m 1` lower triangle only
* `-m 2` upper triangle only
* `-m 3` both triangle / full matrix (default)
### `cgmlst-dists -x N` (short-circuit divergent pairs)
The slowest part of the algorithm is calculating the distance
between two allele vectors. This option will stop comparing as
soon as the distance (differences) exceeds `-x`, and return
the distance as `-x`.
## Issues
Report bugs and give suggesions on the
[Issues page](https://github.com/tseemann/cgmlst-dists/issues)
## Related software
* [chewBBACA](https://github.com/B-UMMI/chewBBACA)
* [snp-dists](https://github.com/tseemann/snp-dists)
## Licence
[GPL Version 3](https://raw.githubusercontent.com/tseemann/cgmlst-dists/master/LICENSE)
## Authors
* [Torsten Seemann](https://github.com/tseemann)