Mercurial > repos > bcclaywell > microbiome_pplacer_suite
comparison preprocessing-wrapper.sh @ 2:ce6db18f5fd3 draft
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| author | bcclaywell |
|---|---|
| date | Thu, 26 Feb 2015 19:31:20 -0500 |
| parents | d4690e65afcd |
| children | 221a97bf686d |
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| 1:c8cc6529038c | 2:ce6db18f5fd3 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 source $1 | |
| 4 | |
| 5 deduplicate_sequences.py \ | |
| 6 --split-map ${SPLIT_MAP} \ | |
| 7 --deduplicated-sequences-file ${DEDUP_INFO} \ | |
| 8 ${INPUT_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}" |