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1 #!/bin/bash
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2
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3 source $1
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4
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5 deduplicate_sequences.py \
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6 --split-map ${SPLIT_MAP} \
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7 --deduplicated-sequences-file ${DEDUP_INFO} \
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8 ${INPUT_SEQS} \
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9 ${DEDUP_SEQS}
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10
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11 # adapted from yapp/bin/refpkg_align
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12 ref_sto=$(taxit rp ${REFPKG} aln_sto)
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13 profile=$(taxit rp ${REFPKG} profile)
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14
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15 sto=$(mktemp -u).sto
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16
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17 cmalign --cpu ${GALAXY_SLOTS:-4} -o "$sto" --sfile "${ALIGNED_SCORES}" --noprob --dnaout "$profile" "${DEDUP_SEQS}" | grep -E '^#'
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18
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19 esl-alimerge --dna --outformat afa "$ref_sto" "$sto" | \
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20 seqmagick convert --output-format fasta --dash-gap - "${ALIGNED_SEQS}"
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