exampleCommands.glue

# List all sequences from Germany or France, from genotypes 1 or 4, collected before 2013
list sequence -w "who_country.id in ('DEU','FRA') and latest_collection_year < 2013 and genotype in ('1','4')" sequenceID who_country.id latest_collection_year genotype

# Within subtype 1a, list sequences from Germany or France before 2013.
alignment AL_1a list member -w "sequence.who_country.id in ('DEU','FRA') and sequence.latest_collection_year < 2013" sequence.sequenceID sequence.who_country.id sequence.gb_isolate sequence.gb_create_date sequence.gb_length

# Which subtype 1a sequences from Germany or France before 2013 cover the various HCV genes?
alignment AL_1a show feature-presence -w "sequence.who_country.id in ('DEU','FRA') and sequence.latest_collection_year < 2013" -r REF_MASTER_NC_004102

# Within subtype 1a, scan sequences from Germany or France before 2013 for any drug resistance in NS5A
alignment AL_1a variation frequency -w "sequence.who_country.id in ('DEU','FRA') and sequence.latest_collection_year < 2013" -r REF_MASTER_NC_004102 -f NS5A -v "is_resistance_associated_variant = true"

# Within subtype 1a, find sequences from Germany or France before 2013 with the NS5A:28V resistance mutation
alignment AL_1a variation member scan -w "sequence.who_country.id in ('DEU','FRA') and sequence.latest_collection_year < 2013" -r REF_MASTER_NC_004102 -f NS5A -v RAS_NS5A_28V --excludeAbsent

# Export a protein alignment of sequences EU155379, EU862823, EU862824 in the NS5A region codon 10 to 45.
module fastaProteinAlignmentExporter export AL_1a -r REF_MASTER_NC_004102 -f NS5A -l 10 45 -w "sequence.sequenceID in ('EU155379','EU862823','EU862824')" --preview