Usage

SeroTools provides methods for querying and comparing serovar names and antigenic formulae, as well as determining the most abundant serovar for a cluster of isolates.

query

Query the White-Kauffmann-Le Minor (WKL) repository by submitting one of more serovar names or antigenic formulas in an input file composed of a single query per line:

$ serotools query -i <input_file>

or as a command line argument:

$ serotools query -s 'Paratyphi A'

Output:

Input        Name         Formula             Match
Paratyphi A  Paratyphi A  I [1],2,12:a:[1,5]  exact

compare

Compare serovar predictions by evaluating multiple states of congruence (exact, congruent, minimally congruent, incongruent). Serovar names and/or antigenic formulae may be submitted in a tab-delimited input file composed of two columns of serovar predictions:

$ serotools compare -i <input_file>

or as command line arguments:

$ serotools compare -1 'Hull' -2 'I 16:b:1,2'

Output:

Serovar1    Name    Formula     Serovar2    Name    Formula     Result
Hull        Hull    I 16:b:1,2  I 16:b:1,2  Hull    I 16:b:1,2  exact

cluster

Determine the most abundant serovar(s) for one or more clusters of isolates. Input data must be submitted in the form of a tab-delimited file in which each line consists of a cluster ID and one serovar as follows:

Input File - example.txt:

cluster1    Dunkwa
cluster1    Dunkwa
cluster1    Utah
cluster2    Hull

$ serotools cluster -i example.txt

Output:

ClusterID   ClusterSize Input   Name    Formula      P_Exact  P_Congruent   P_MinCon
cluster1    2           Dunkwa  Dunkwa  I 6,8:d:1,7  0.6667   0.6667        0.6667
cluster2    1           Hull    Hull    I 16:b:1,2   1.0      1.0           1.0