Mercurial > repos > bcclaywell > microbiome_pplacer_suite
comparison 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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| children |
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| 2:ce6db18f5fd3 | 3:221a97bf686d |
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| 1 #!/bin/bash | |
| 2 | |
| 3 source $1 | |
| 4 | |
| 5 # adapted from yapp/bin/refpkg_align | |
| 6 ref_sto=$(taxit rp ${REFPKG} aln_sto) | |
| 7 profile=$(taxit rp ${REFPKG} profile) | |
| 8 | |
| 9 sto=$(mktemp -u).sto | |
| 10 | |
| 11 cmalign --cpu ${GALAXY_SLOTS:-4} -o "$sto" --sfile "${ALIGNED_SCORES}" --noprob --dnaout "$profile" "${INPUT_SEQS}" | grep -E '^#' | |
| 12 | |
| 13 esl-alimerge --dna --outformat afa "$ref_sto" "$sto" | \ | |
| 14 seqmagick convert --output-format fasta --dash-gap - "${ALIGNED_SEQS}" |