byconaut

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

Installation

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.

Database setup

Option A: examplez from <rsrc/mongodump>

1. download <rsrc/mongodump/examplez.zip>
2. unpack somewhere & restore with (your paths etc.):

mongosh examplez --eval 'db.dropDatabase()'
mongorestore --db examplez ./rsrc/mongodump/examplez/

3. proceed w/ step 4 ... below

Option B: Create your own databases

1. Create database and variants collection
2. update the local bycon installation for your database information andlocal parameters
   • database name(s)
   • filter_definitions for parameter mapping
3. Create metadata collections - callsets, biosamples and individuals
4. Create statusmaps and CNV statistics for the callsets collection
   • only relevant for CNV database use cases
5. Create the collations collection which uses filter_definitions and the corresponding values to aggregate information for query matching, term expansion ...
6. Create frequencymaps for binned CNV data
   • relies on existence of statusmaps in callsets and collations
   • only needed for CNV data

Server services

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.

Data maintenance scripts

callsetsStatusmapsRefresher (CNV)

The callsetsStatusmapsRefresher 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).

Examples

• bin/callsetsStatusmapsRefresher.py -d examplez

collationsCreator

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.

Examples

• bin/collationsCreator.py -d examplez --collationTypes "icdom,icdot"
• bin/collationsCreator.py -d progenetix

frequencymapsCreator (CNV)

frequencymaps contain pre-computed frequencies for CNV data, aggregating the binned statusmaps data from all callsets belonging to a given collation.

Examples

• bin/frequencymapsCreator.py -d examplez

Utility apps

ISCNsegmenter

Examples

• bin/ISCNsegmenter.py -i imports/ccghtest.tab -o exports/cghtest-with-histo.pgxseg