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get-frequencies.glue
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# Get frequencies
# Set console output format
console set cmd-output-file-format tab
# Get frequencies in placental 1's
console set next-cmd-output-file ifnl-mammal-bp1-freqs-orf.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f orf -w "sequence.gene_id like 'Placental1%'"
console set next-cmd-output-file ifnl-mammal-bp1-freqs-exposed_residues.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f exposed_residues -w "sequence.gene_id like 'Placental1%'"
console set next-cmd-output-file ifnl-mammal-bp1-freqs-il10r2_binding_surface.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f il10r2_binding_surface -w "sequence.gene_id like 'Placental1%'"
console set next-cmd-output-file ifnl-mammal-bp1-freqs-ifnlr1_binding_surface.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f ifnlr1_binding_surface -w "sequence.gene_id like 'Placental1%'"
console set next-cmd-output-file ifnl-mammal-bp1-freqs-buried_residues.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f buried_residues -w "sequence.gene_id like 'Placental1%'"
console set next-cmd-output-file ifnl-mammal-bp1-freqs-exposed_nonbinding_residues.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f exposed_nonbinding_residues -w "sequence.gene_id like 'Placental1%'"
console set next-cmd-output-file ifnl-mammal-bp1-freqs-non_receptor_binding.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f non_receptor_binding -w "sequence.gene_id like 'Placental1%'"
# Get frequencies in placental 2's
console set next-cmd-output-file ifnl-mammal-bp2-freqs-orf.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f orf -w "sequence.gene_id like 'Placental2%'"
console set next-cmd-output-file ifnl-mammal-bp2-freqs-exposed_residues.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f exposed_residues -w "sequence.gene_id like 'Placental2%'"
console set next-cmd-output-file ifnl-mammal-bp2-freqs-il10r2_binding_surface.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f il10r2_binding_surface -w "sequence.gene_id like 'Placental2%'"
console set next-cmd-output-file ifnl-mammal-bp2-freqs-ifnlr1_binding_surface.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f ifnlr1_binding_surface -w "sequence.gene_id like 'Placental2%'"
console set next-cmd-output-file ifnl-mammal-bp2-freqs-buried_residues.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f buried_residues -w "sequence.gene_id like 'Placental2%'"
console set next-cmd-output-file ifnl-mammal-bp2-freqs-exposed_nonbinding_residues.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f exposed_nonbinding_residues -w "sequence.gene_id like 'Placental2%'"
console set next-cmd-output-file ifnl-mammal-bp2-freqs-non_receptor_binding.tsv
alignment AL_IFNL_MAMMAL_B amino-acid frequency -r REF_IFNL_Mammal_b_MASTER -f non_receptor_binding -w "sequence.gene_id like 'Placental2%'"