search

m2ms / fragalysis-frontend

The React, Redux frontend built by webpack
Other
1 stars 2 forks source link

Aggregate standardised test data for XCA & loader #1588

Open mwinokan opened 1 day ago

mwinokan commented 1 day ago

@mwinokan please give @tdudgeon some paths to test data. N.B. the original data should be copied in case it is archived to tape

@tdudgeon then please prepare some unit tests based on this

mwinokan commented 1 day ago

@tdudgeon here are some config.yaml examples that have been used to run XCA recently:

Target config.yaml
A71EV2A /dls/labxchem/data/lb32627/lb32627-66/processing/analysis/xchem_align_uploads/config.yaml
CHIKV_Mac /dls/labxchem/data/lb32633/lb32633-6/processing/analysis/xchemalign/config.yaml
FatA /dls/labxchem/data/lb36049/lb36049-1/processing/lb30602-66/processing/analysis/outputs/config.yaml
Flavi_NS5_RdRp /dls/labxchem/data/lb32627/lb32627-71/processing/analysis/DENV-ZIKV-xchemalign/config.yaml
CpKRS /dls/labxchem/data/lb36049/lb36049-7/processing/analysis/xchemalign/config.yaml

Please let me know if you need any other paths.

Again please also store the original data somewhere else so that we are not affected by unwanted archiving

tdudgeon commented 8 hours ago

@mwinokan can you confirm that none of those dataset need to be treated as confidential.

mwinokan commented 8 hours ago

@tdudgeon Some are definitely entirely confidential, and likely more have at least a confidential subset.

tdudgeon commented 7 hours ago

@mwinokan I don't have access to the FatA or CpKRS data. And BTW there are errors in the config.yaml for Flavi_NS5_RdRp (panddas paths are not relative)

tdudgeon commented 6 hours ago

@mwinokan @ConorFWild There are problems with the A71EV2A data. It looks like a new reference structure (A71_2A_new_model_x2721_4.1_ref3) has recently been added to this target, but that PDB file is missing the C-terminal residue compared to the other structures. This seems to cause aligner to blow up. Commenting out that reference doesn't help as that structures is used as a reference in assemblies.yaml.

You get an error like this: AssertionError: There are no valid reference positions to align. You may want to check residues numbers are the same between your assembly reference and datasets.

tdudgeon commented 6 hours ago

@mwinokan The info for Flavi_NS5_RdRp does not seem to be correct. The config.yaml file you mention is /dls/labxchem/data/lb32627/lb32627-71/processing/analysis/DENV-ZIKV-xchemalign/config.yaml but that file refers to data in /dls/labxchem/data/lb32633/lb32633-1 which seems to be a completely different target.