Small tool to setup a local variant database.
Right now locusdb uses mongodb as backend for storing variants but there should not be a huge difference to use another database manager.
pip install loqusdb
or
$git clone https://github.com/moonso/loqusdb
$cd loqusdb
$pip install --editable .
Tool to keep track of what variants that have been seen and in what families they have been observed. This is NOT a tool to create a true frequency database. It will basically count the number of times we have seen a variant in any individual. We will also keep track of the variants that have been seen in a homozygous or hemizygous state.
Variants are stored by providing a vcf file and a (ped or ped like)family file.
Loqusdb will first check if the vcf file looks ok.
The tool will then check all variants if they have been observed in any of the individuals in the family.
When the variants are added:
- Either the variant exists, in this case we increase the number of observations with one
- Or this variant has not ben seen before, then the variant is added to database
$ loqusdb
Usage: loqusdb [OPTIONS] COMMAND [ARGS]...
loqusdb: manage a local variant count database.
Options:
-db, --database TEXT [default: loqusdb]
-u, --username TEXT
-p, --password TEXT
-port, --port INTEGER Specify the port where to look for the mongo
database. [default: 27017]
-h, --host TEXT Specify the host where to look for the mongo
database. [default: localhost]
-b, --backend [mongo] Specify what backend to use. [default: mongo]
-c, --conn_host TEXT Used for testing. [default: mongodb://]
-l, --logfile PATH Path to log file. If none logging is printed to
stderr.
-v, --verbose
--version Show the version and exit.
--help Show this message and exit.
Commands:
delete Delete the variants of a case
load Load the variants of a case The loading is...
wipe Wipe the entire db
export Export the variants in a database
The collections looks like:
Case
{
'case_id': 'case_id',
'vcf_path': 'path_to_vcf'
}Variant
{
'_id': 'variant_id',
'chrom': 'CHROM',
'pos': postition,
'homozygote': number_of_homozygotes,
'hemizygote': number_of_hemizygotes,
'observations': number_of_observations,
'families': ['family_id', ...]
}