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 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

Related software

• chewBBACA
• snp-dists

Licence

GPL Version 3

Authors

• Torsten Seemann