Mercurial > repos > bcclaywell > microbiome_pplacer_suite

diff 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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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alignment-wrapper.sh	Wed Mar 25 16:39:10 2015 -0400
@@ -0,0 +1,14 @@
+#!/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}"