Mercurial > repos > bcclaywell > microbiome_pplacer_suite

annotate alignment-wrapper.sh @ 3:221a97bf686d draft

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author bcclaywell
date Wed, 25 Mar 2015 16:39:10 -0400
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1 #!/bin/bash
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3 source $1
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5 # adapted from yapp/bin/refpkg_align
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6 ref_sto=$(taxit rp ${REFPKG} aln_sto)
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7 profile=$(taxit rp ${REFPKG} profile)
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9 sto=$(mktemp -u).sto
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11 cmalign --cpu ${GALAXY_SLOTS:-4} -o "$sto" --sfile "${ALIGNED_SCORES}" --noprob --dnaout "$profile" "${INPUT_SEQS}" | grep -E '^#'
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13 esl-alimerge --dna --outformat afa "$ref_sto" "$sto" | \
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14 seqmagick convert --output-format fasta --dash-gap - "${ALIGNED_SEQS}"