The byconaut
package contains scripts for data processing for and based on the
bycon
package. The main use cases are:
- generation of utility collections for the standard Progenetix data model
collations
frequencymaps
provide binned CNV frequency values for samples belonging to a given collation code
- I/O & transformations for
bycon
generated files
byconaut
depends on the bycon
package which can be downloaded from its
repository. Please see the repository
and the corresponding documentation site.
While there is also a pip
installation possible over pip3 install bycon
this will not include the local configuration files necessary e.g. for
processing the databases.
- download <rsrc/mongodump/examplez.zip>
- unpack somewhere & restore with (your paths etc.):
mongosh examplez --eval 'db.dropDatabase()'
mongorestore --db examplez ./rsrc/mongodump/examplez/
- proceed w/ step 4 ... below
- Create database and variants collection
- update the local
bycon
installation for your database information andlocal parameters- database name(s)
filter_definitions
for parameter mapping
- Create metadata collections -
analyses
,biosamples
andindividuals
- Create
statusmaps
and CNV statistics for the analyses collection- only relevant for CNV database use cases
- Create the
collations
collection which usesfilter_definitions
and the corresponding values to aggregate information for query matching, term expansion ... - Create
frequencymaps
for binned CNV data- relies on existence of
statusmaps
inanalyses
andcollations
- only needed for CNV data
- relies on existence of
Since version 1.0.55
(2023-06-22) additional "services" may be installed from
the byconaut
repository using the
install.py
utility script. Please edit the install.yaml
configuration accordingly.
The analysesStatusmapsRefresher
script creates CNV status data for binned
genomic intervals, for each CNV callset (i.e. the CNV data of all corresponding
variants from the same experiment/sample).
bin/analysesStatusmapsRefresher.py -d examplez
collations
provide aggregate data for all samples etc. matching a given
classification, external reference or other entity code, including hierarchy
data for term expansion when matching the code. The hierarchy data is provided
in rsrc/classificationTrees/__filterType__/numbered-hierarchies.tsv
as a list
of ordered branches in the format code | label | depth | order
.
bin/collationsCreator.py -d examplez --collationTypes "icdom,icdot"
bin/collationsCreator.py -d progenetix
frequencymaps
contain pre-computed frequencies for CNV data, aggregating
the binned statusmaps data from all analyses belonging to a given collation.
bin/frequencymapsCreator.py -d examplez
bin/ISCNsegmenter.py -i imports/ccghtest.tab -o exports/cghtest-with-histo.pgxseg