Mercurial > repos > bcclaywell > microbiome_pplacer_suite

view 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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#!/bin/bash

source $1

# adapted from yapp/bin/refpkg_align
ref_sto=$(taxit rp ${REFPKG} aln_sto)
profile=$(taxit rp ${REFPKG} profile)

sto=$(mktemp -u).sto

cmalign --cpu ${GALAXY_SLOTS:-4} -o "$sto" --sfile "${ALIGNED_SCORES}" --noprob --dnaout "$profile" "${INPUT_SEQS}" | grep -E '^#'

esl-alimerge --dna --outformat afa "$ref_sto" "$sto" | \
    seqmagick convert --output-format fasta --dash-gap - "${ALIGNED_SEQS}"