Mercurial > repos > bcclaywell > microbiome_pplacer_suite
comparison preprocessing-wrapper.sh @ 3:221a97bf686d draft
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author | bcclaywell |
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date | Wed, 25 Mar 2015 16:39:10 -0400 |
parents | d4690e65afcd |
children |
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2:ce6db18f5fd3 | 3:221a97bf686d |
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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}" |