The mason components needed to run the solgenomics.net website
solgenomics / bio-chado-loader Goto Github PK
View Code? Open in Web Editor NEWLoad biological data into the Chado database with Bio::Chado::Schema
Load biological data into the Chado database with Bio::Chado::Schema
Move class vars to Loader to conform to Fasta.pm structure.
Add the test code from gff3_chado.t including GFF. Should compare final featurelocs from CHADO with correct set. Compare featurelocs pre and post edit.
Check if any names are still malformed after fix. See Aure's stand-alone script test system. Compare featurelocs pre and post edit.
Lots of features (mRNA and exon) records with feature.uniquename = name-<feature_id> format. Results in exception in bio-chado-loader. Print err while comparing GFF records to cache.
Need to break up the inserts into 1k feature blocks
Chado has no CDS or UTR. Only polypeptide starting at beginning of 1st CDS and ending at last CDS. Add functionality to convert CDS features to polypeptide features.
#4 does not cut it.
Get the mRNA name from feature_relationship and use it for the name and uniquename
Change perms for test_usr so that it can be used for testing all operations.
Most expensive atm
Some handlers are not tested. Many routines contain same tests
How to handle update of auto<feature_id> rows?
Still using srcfeature_id from old featureloc. Should be srcfeature_id for new chr backbone which needs to be inserted in feature table beforehand.
Make sure that fasta seqs with only feature.uniquename or ID are accepted.
Should be runnable with /usr/local/bin/bin/mx-run
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