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rabvProject.glue
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rabvProject.glue
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delete project rabv
create project rabv "Core GLUE project for the rabies virus (RABV)" --minVersion 1.1.107
schema-project rabv
run file glue/rabvSchemaExtensions.glue
exit
project rabv
run file glue/rabvProjectSettings.glue
run file glue/rabvModules.glue
run file glue/m49_countries/populateM49All.glue
# Import sources containing reference sequences
import source sources/ncbi-refseqs
import source sources/ncbi-refseqs-outgroup
# Define features
run file glue/rabvFeatures.glue
# Populate sequence table fields from GenBank XML
module rabvGenbankXmlPopulator populate -w "source.name in ('ncbi-refseqs', 'ncbi-refseqs-outgroup')"
# Import data from tabular
module textFilePopulatorRefSet populate -f tabular/reference-set-data.tsv
# this alignment was generated by rabvAlign509RefseqsMafft.glue, followed by
# some hand-alignment, to remove incorrect large gaps introduced at the end of a few sub-genomic sequences.
module blastFastaAlignmentImporter
import AL_UNC_509_REFSEQS_HM -f alignments/alUnc509RefseqsMafftHandModified.fna
exit
# Create reference sequences
run file glue/rabvReferences.glue
# Add feature locations to the reference sequences
run script glue/rabvAddFeatureLocations.js
# Import alignment tree
run file glue/rabvAlignmentTree.glue
# Check feature locations
#run script glue/rabvCheckFeatureLocations.js
# hack: the INFORMATIONAL metatag has overloaded semantics
# on the one hand if it is not 'true' it interferes with how inherit feature-location works,
# on the other hand, we want it unset so that people can download whole-genome nucleotide alignments
feature whole_genome unset metatag INFORMATIONAL
# Import phylogeny
run file glue/rabvImportPhylogeny.glue
# Validate
validate
exit