|
sonar setup
|
|
|
--db FILE
|
specify the name of the new database
|
|
--gbk FILE
|
set a custom reference based on the specified Genbank file [opt.]
|
|
-a
--auto-create |
add pre-defined sample properties to the new database [opt.]
|
|
sonar info
|
|
|
--db FILE
|
specify name of the database
|
|
sonar import
|
to import data
|
|
--db FILE
|
specify name of the database
|
|
--fasta FILE [FILE, ...]
|
specify fasta file to import sequences [opt]
|
|
--tsv FILE [FILE, ...]
|
specify tab-delimited text file to import meta information [opt]
|
|
--cols STR [STR, ...]
|
link properties with tsv columns in the form of
prop_name=col_header [opt] |
|
--no-autodetect
|
do not auto-link properties with tsv columns based on identical names [opt]
|
|
--no-update
|
skip data of existing samples [opt]
|
|
--cache DIR
|
specify a folder to cache import data [opt]
|
|
-t INT
--threads INT |
specify number of threads / cpus to use [opt]
|
|
sonar delete
|
to delete sample(s)
|
|
--db FILE
|
specify name of the database
|
|
--sample STR [STR, ...]
|
specify names of samples to delete [opt]
|
|
--sample-file FILE
|
specify file containing names of samples to delete [opt]
|
|
--force FILE
|
force deletion and skip user confirmation [opt]
|
|
sonar optimize
|
}to clean database
|
|
--db FILE
|
specify name of the database
|
|
sonar db-upgrade
|
upgrade database to the latest version
|
|
--db FILE
|
specify name of the database
|
|
sonar list-prop
|
to list available properties
|
|
--db FILE
|
specify name of the database
|
|
sonar add-prop
|
add new property
|
|
--db FILE
|
specify name of the database
|
|
--name STR
|
specify new property name matching to [A-Z][A-Z0-9_]+
|
|
--descr STR
|
provide a short property description
|
|
--dtype STR
|
specify data type
|
|
--qtype STR
|
specify query type [opt]
|
|
--default
|
specify default value [opt]
|
|
sonar delete-prop
|
delete property
|
|
--db FILE
|
specify name of the database
|
|
--name STR
|
specify new property name
|
|
--force
|
force deletion without user confirmation [opt]
|
|
sonar match
|
|
|
--sample STR [STR, ...]
|
consider given samples only [opt]
|
|
--sample-file *FILE
|
consider samples listed in the given file only [opt]
|
|
--profile STR [STR, ...]
|
match given mutation profile (use argument multiple times to define alternate profiles) [opt]
|
|
--PROP VALUE [VALUE, ...]
|
filter based on sample property (PROP has to be replaced by the actual property name) [opt]
|
|
--with-sublineage PROP
|
include pangolin sub-lineages for the given property [opt]
Use sonar update-lineage-info to update lineage info before |
|
--showNX
|
show uninformative variant allels for genome profiles [opt]
|
|
--out-cols STR [STR, ...]
|
specify columns to show (for tsv and csv only) [opt]
|
|
--count
|
show number of matching genomes only [opt]
|
|
--format {csv, tsv, vcf}
|
specify the output format [opt]
|
|
-o FILE
--out FILE |
write output to the given file [opt]
|
|
Genome level
|
Protein level
|
|
|
Substitution
|
REFposALT
e.g. A3451T |
PROT:REFposALT
e.g. A3451T |
|
Insertion
|
REFposALT
e.g. A4057TGAT |
PROT:REFposALT
e.g. N:A34AK |
|
1-bp Deletion
|
del:pos
e.g. del:11288 |
PROT:del:pos
e.g. ORF1ab:del:300 |
|
multi-bp Deletion
|
del:start-end
e.g. del:112-115 |
PROT:del:start-end
e.g. S:del:68-69 |
|
Deletion with fixed coordinates
|
del:=start-=end
e.g. del:=8-=11 |
PROT:del:=start-=end
e.g. S:del:=68-=69 |
|
integer
|
for storing integers
|
|
float
|
for storing decimal numbers
|
|
text
|
for storing strings
|
|
dates
|
for storing dates in the form YYYY-MM-DD
|
|
zip
|
for storing zip codes
|
|
Operator
|
Description
|
Valid data type
|
|
>
|
larger than (e.g. >1)
|
integer, float, date
|
|
<
|
smaller than (e.g. <1)
|
integer, float, date
|
|
>=
|
larger than or equal to (e.g. >=1)
|
integer, float, date
|
|
<=
|
smaller than or equal to (e.g. <=1)
|
integer, float, date
|
|
!=
|
different than (e.g. !=1)
|
integer, float, date
|
|
:
|
from:to range (e.g.
2021-01-01:2021-12-31) |
integer, float, date
|
|
^
|
not the same as (e.g. ^B.1.1.7)
|
text
|
|
%
|
wildcard standing for any character(s) (e.g. %human%)
|
text
|
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