Mercurial > repos > bcclaywell > microbiome_pplacer_suite

comparison preprocessing-wrapper.sh @ 3:221a97bf686d draft

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author bcclaywell
date Wed, 25 Mar 2015 16:39:10 -0400
parents d4690e65afcd
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2:ce6db18f5fd3 3:221a97bf686d
5 deduplicate_sequences.py \ 5 deduplicate_sequences.py \
6 --split-map ${SPLIT_MAP} \ 6 --split-map ${SPLIT_MAP} \
7 --deduplicated-sequences-file ${DEDUP_INFO} \ 7 --deduplicated-sequences-file ${DEDUP_INFO} \
8 ${INPUT_SEQS} \ 8 ${INPUT_SEQS} \
9 ${DEDUP_SEQS} 9 ${DEDUP_SEQS}
10
11 # adapted from yapp/bin/refpkg_align
12 ref_sto=$(taxit rp ${REFPKG} aln_sto)
13 profile=$(taxit rp ${REFPKG} profile)
14
15 sto=$(mktemp -u).sto
16
17 cmalign --cpu ${GALAXY_SLOTS:-4} -o "$sto" --sfile "${ALIGNED_SCORES}" --noprob --dnaout "$profile" "${DEDUP_SEQS}" | grep -E '^#'
18
19 esl-alimerge --dna --outformat afa "$ref_sto" "$sto" | \
20 seqmagick convert --output-format fasta --dash-gap - "${ALIGNED_SEQS}"