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get_alignments.glue
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# Get alignments
delete module ifnlFastaProteinAlignmentExporter
create module -f modules/build/core/ifnlFastaProteinAlignmentExporter.xml
# Export alignments for placental 1 members
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f orf -w "sequence.gene_id like 'Placental1%'" -e -o ifnl-mammal-bp1-orf.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f exposed_residues -w "sequence.gene_id like 'Placental1%'" -e -o ifnl-mammal-bp1-exposed_residues.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f il10r2_binding_surface -w "sequence.gene_id like 'Placental1%'" -e -o ifnl-mammal-bp1-il10r2_binding_surface.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f ifnlr1_binding_surface -w "sequence.gene_id like 'Placental1%'" -e -o ifnl-mammal-bp1-ifnlr1_binding_surface.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f buried_residues -w "sequence.gene_id like 'Placental1%'" -e -o ifnl-mammal-bp1-buried_residues.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f exposed_nonbinding_residues -w "sequence.gene_id like 'Placental1%'" -e -o ifnl-mammal-bp1-exposed_nonbinding_residues.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f non_receptor_binding -w "sequence.gene_id like 'Placental1%'" -e -o ifnl-mammal-bp1-non_receptor_binding.aln.fasta
# Export alignments for placental 2 members
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f orf -w "sequence.gene_id like 'Placental2%'" -e -o ifnl-mammal-bp2-orf.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f exposed_residues -w "sequence.gene_id like 'Placental2%'" -e -o ifnl-mammal-bp2-exposed_residues.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f il10r2_binding_surface -w "sequence.gene_id like 'Placental2%'" -e -o ifnl-mammal-bp2-il10r2_binding_surface.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f ifnlr1_binding_surface -w "sequence.gene_id like 'Placental2%'" -e -o ifnl-mammal-bp2-ifnlr1_binding_surface.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f buried_residues -w "sequence.gene_id like 'Placental2%'" -e -o ifnl-mammal-bp2-buried_residues.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f exposed_nonbinding_residues -w "sequence.gene_id like 'Placental2%'" -e -o ifnl-mammal-bp2-exposed_nonbinding_residues.aln.fasta
module ifnlFastaProteinAlignmentExporter export AL_IFNL_MAMMAL_B -r REF_IFNL_Mammal_b_MASTER -f non_receptor_binding -w "sequence.gene_id like 'Placental2%'" -e -o ifnl-mammal-bp2-non_receptor_binding.aln.fasta