progenetix / bycon

Bycon - A Python Based Beacon API (beacon-project.io) implementation leveraging the Progenetix (progenetix.org) data model

Bycon - a Python-based environment for the Beacon v2 genomics API

The bycon project - at least at its current stage - is a mix of Progenetix (i.e. GA4GH object model derived, MongoDB implemented) - data management, and the implementation of middleware & server for the Beacon API.

In its current state the bycon package is undergoing a transition from resource specific to general use environment. There is still some entanglement between code and use case specific definitions (e.g. database definitions inside the distribution) though this is (early 2023) in a process of "disentanglement".

More Documentation

Documentation has been moved to bycon.progenetix.org. W/ the rapid code development it is recommended to keep following the Changes page.

Installation

The installation is documented on the website (and in the page's Markdown source here).

Since version 1.0.55 (2023-06-22) additional "services" may be installed from the byconaut repository.

bycon's Issues

KeyError: 'reference_bases' (when getting data from the progenetix website)

Hello,

I have troubles to get ".pgxseg" files from both the R package and the website. The table I download from the website always has this python error referring the "bycon" package :

Traceback (most recent call last):
  File "/Library/WebServer/cgi-bin/bycon/beaconServer/beacon.py", line 19, in main
    beacon()
  File "/Library/WebServer/cgi-bin/bycon/beaconServer/beacon.py", line 65, in beacon
    beacon_data_pipeline(byc, f)
  File "/usr/local/lib/python3.10/site-packages/bycon/lib/service_utils.py", line 59, in beacon_data_pipeline
    run_result_sets_beacon(byc)
  File "/usr/local/lib/python3.10/site-packages/bycon/lib/service_utils.py", line 287, in run_result_sets_beacon
    check_alternative_single_set_deliveries(ds_id, r_s_res, byc)
  File "/usr/local/lib/python3.10/site-packages/bycon/lib/service_utils.py", line 355, in check_alternative_single_set_deliveries
    check_alternative_variant_deliveries(ds_id, byc)
  File "/usr/local/lib/python3.10/site-packages/bycon/lib/service_utils.py", line 744, in check_alternative_variant_deliveries
    export_pgxseg_download(ds_id, byc)
  File "/usr/local/lib/python3.10/site-packages/bycon/lib/export_file_generation.py", line 165, in export_pgxseg_download
    print_variant_pgxseg(v, byc)
  File "/usr/local/lib/python3.10/site-packages/bycon/lib/export_file_generation.py", line 173, in print_variant_pgxseg
    print( pgxseg_variant_line(v, byc) )
  File "/usr/local/lib/python3.10/site-packages/bycon/lib/export_file_generation.py", line 203, in pgxseg_variant_line
    pv["reference_bases"],
KeyError: 'reference_bases'

It may be linked with the recent update since I did not had these issues on Friday ?

Thanks a lot for your great tool and your help !

Optimize loading

The services app is a loader / redirect for a most of the bycon apps, thereby guaranteeing stable paths etc.

One problem with this approach is that all the apps are loaded as packages, not only the called one:

bycon/bin/services.py

Line 12 in 23d8975

from bin.biosamples import biosamples

TODO: implement a dynamic loader, which only loads the selected package (after

bycon/bin/services.py

Line 75 in 23d8975

f = p_items[ i ]

).

start and end range values

Hi,
I am wondering if in this query:
https://bycon.progenetix.org/query?datasetIds=arraymap&assemblyId=GRCh38&includeDatasetResponses=ALL&requestType=variantCNVrequest&referenceName=9&variantType=DEL&start=20000000&start=21975097&end=21967753&end=23000000&filters=icdom-94403
it will not be easier instead of duplicating the "Start" and "End" properties (to define a range for a region of interest) to have only one attribute "Start" or "End" with a range definition with a comma as following:
https://bycon.progenetix.org/query?datasetIds=arraymap&assemblyId=GRCh38&includeDatasetResponses=ALL&requestType=variantCNVrequest&referenceName=9&variantType=DEL&start=20000000,21975097&end=21967753,23000000&filters=icdom-94403
All the best
David

results need to be sorted in VCF4.4 for a specific biosample

Hello, I have noticed that VCF data are not sorted
Best
David

VCF4.4

Hello,
Genome version should be indicated in the VCF for a specific dataset output
David

Chromosome name is missing in VCF4.4 experimental feature

Hello,
I have noticed that the chromosome name is missing in the VCF4.4 generated for a specific individual.
Here is an example of what I am getting

##fileformat=VCFv4.4
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=DEL,Description="Deletion">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record">
##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant">
##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint">
##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM   POS   ID   REF   ALT   QUAL   FILTER   FORMAT   INFO   onekgbs-NA12878
.   54338076   .   .   <DEL>   .   PASS   GT   IMPRECISE;SVCLAIM=D;END=54340326;SVLEN=2251   0/1
.   36123036   .   .   <DUP>   .   PASS   GT   IMPRECISE;SVCLAIM=D;END=36125764;SVLEN=2729   0/1
.   156373723   .   .   <DEL>   .   PASS   GT   IMPRECISE;SVCLAIM=D;END=156375723;SVLEN=2001   0/1
.   63092508   .   .   <DEL>   .   PASS   GT   IMPRECISE;SVCLAIM=D;END=63094701;SVLEN=2194   0/1
.   88859135   .   .   <DEL>   .   PASS   GT   IMPRECISE;SVCLAIM=D;END=88886287;SVLEN=27153   0/1