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btvProject.glue
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btvProject.glue
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delete project btv
create project btv "A GLUE project for Bluetongue virus (BTV)" --minVersion 1.1.107
run file glue/btvSchemaExtensions.glue
project btv
# settings file, including version
run file glue/btvProjectSettings.glue
# create modules from files
run file glue/btvModules.glue
# WHO regions / countries etc (M49 standard)
run file glue/who_countries/populateWhoCountries.glue
# features.
run file glue/btvFeatures.glue
run file glue/btvFGFeatures.glue
# per segment refseqs
import source sources/ncbi-s1-refseqs
import source sources/ncbi-s2-refseqs
import source sources/ncbi-s3-refseqs
import source sources/ncbi-s4-refseqs
import source sources/ncbi-s5-refseqs
import source sources/ncbi-s6-refseqs
import source sources/ncbi-s7-refseqs
import source sources/ncbi-s8-refseqs
import source sources/ncbi-s9-refseqs
import source sources/ncbi-s10-refseqs
# create references based on per-segment JSONs
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S1_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S2_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S3_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S4_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S5_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S6_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S7_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S8_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S9_clade_structure_and_refs.json
module btvCladeStructureProcessor invoke-function createGlueReferenceSequences json/S10_clade_structure_and_refs.json
# create per-segment master reference feature locations
run file glue/btvMasterReferenceFeatureLocs.glue
# Import NCBI curated sequence set
import source sources/ncbi-curated
# Import NCBI outgroup sequence set
import source sources/ncbi-outgroup
# these ensure we have accurate feature annotations for the outgroup sequences.
# Temporarily commented out as these references are not in
# the GENO alignments, therefore codon labeling cannot work and feature location validation fails.
# run file glue/btvOutgroupReferences.glue
# load publications
run script glue/btvLoadPublications.js
# import sequence-associated data from GenBank xml and tabular
run file glue/btvSequenceAssociatedData.glue
# various sets of unconstrained alignments used for phylogenetic analysis
run script glue/btvImportCompleteSegNtAlignments.js
run script glue/btvImportOutgroupCodonAlignments.js
run script glue/btvImportRaxmlNgPhyloTrees.js
run script glue/btvImportGenoCodonAlignments.js
# Trees associated with the BTV_OUTG_CODON... alignments as side data.
# RAxML-NG generated tree (500 bootstraps).
# run script glue/btvProcessRaxmlNgPhyloTrees.js
# From these, "display trees" with cluster assignments can be generated, suitable for loading into FigTree.
# run script glue/generateClusterAnnotations.js
# derive feature locations for non-master references across all segments.
run script glue/btvAddFeatureLocations.js
# create alignment trees for all segments
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S1_clade_structure_and_refs.json BTV_GENO_CODON_1
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S2_clade_structure_and_refs.json BTV_GENO_CODON_2
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S3_clade_structure_and_refs.json BTV_GENO_CODON_3
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S4_clade_structure_and_refs.json BTV_GENO_CODON_4
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S5_clade_structure_and_refs.json BTV_GENO_CODON_5
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S6_clade_structure_and_refs.json BTV_GENO_CODON_6
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S7_clade_structure_and_refs.json BTV_GENO_CODON_7
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S8_clade_structure_and_refs.json BTV_GENO_CODON_8
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S9_clade_structure_and_refs.json BTV_GENO_CODON_9
module btvCladeStructureProcessor invoke-function createAlignmentTree json/S10_clade_structure_and_refs.json BTV_GENO_CODON_10
# import reference phylogenies
run script glue/btvImportReferencePhylogenies.js
# genotype segment urated sequences using placement files,
# add them to the alignment tree and recompute alignments.
run script glue/btvGenotypeCuratedSequences.js
# record feature presence
run file glue/recordFeaturePresence.glue
validate
exit