Export results¶
When the database is complete and validated, you can export results for futher analysis.
Distance¶
A matrix of cgMLST distances can be computed from the database and defined as the number of different alleles between each pair of two strains, omitting the missing data.
#Strain 33_PA 34_PA 35_PA 61_PA 84_PA 98_PA
33_PA 0 39 37 25 20 23
34_PA 39 0 5 33 35 39
35_PA 37 5 0 31 33 37
61_PA 25 33 31 0 22 27
84_PA 20 35 33 22 0 21
98_PA 23 39 37 27 21 0
wgMLST distance --help
Usage: wgMLST distance [OPTIONS] DATABASE
Extracts a distance matrix from a wgMLST DATABASE.
Options:
-m, --mincover INTEGER Minimun number of strains found to retain a gene
(default:0)
-k, --keep Keeps only gene with different alleles (omit
missing).
-d, --duplicate Keeps duplicate genes (default remove).
-V, --inverse Keeps only gene that do not match the filter of
mincover or keep options.
Warning
To have correct distance calculation, you need to filter genes with low frequency observations. See validate to have more informations on -m option.
MLST¶
The MLST profiles can be also exported. The number indicated the allele id in the database. An formatted version compatible with grapetree can be defined.
#GeneId 33_PA 34_PA 35_PA 61_PA 84_PA 98_PA
PA0120 3918 3918 3918 3918 3918 3918
PA0527 3963 3963 3963 3963 3963 3963
PA0691 3954 3954 3954 8945 3954 3954
PA0935 3910 3910 3910 3910 3910 3910
...
wgMLST mlst --help
Usage: wgMLST mlst [OPTIONS] DATABASE
Extracts an MLST table from a wgMLST DATABASE.
Options:
...
-f, --form [default|grapetree] Specify format of output
Note
Similarly to distance, the gene export on this mlst table can be defined with -m, -k, and -d options.