Mercurial > repos > bcclaywell > microbiome_pplacer_suite
view usearch-wrapper.sh @ 6:3c50a937d7c1 draft
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author | bcclaywell |
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date | Wed, 15 Apr 2015 19:14:23 -0400 |
parents | d4690e65afcd |
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#!/bin/bash source $(dirname $0)/util.sh source $1 RDP_SEQS="/shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/rdp/10_31/tax_filter/filtered/rdp_10_31.filter.fasta" RDP_SEQINFO="/shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/rdp/10_31/tax_filter/filtered/rdp_10_31.filter.seq_info.csv" sqlite3 -csv -header ${CLASS_DB} <<EOF > usearch_meta.csv SELECT pn.name, CAST(pn.mass AS INT) count, tax_id, tax_name, taxa.rank FROM multiclass_concat JOIN taxa USING (tax_id) JOIN placement_names pn USING (placement_id, name) WHERE want_rank = 'species'; EOF romp -v usearch_clusters \ --usearch-quietly \ --query-group tax_id \ --query-duplication count \ --database-name seqname \ --database-group tax_id \ ${INPUT_SEQS} \ usearch_meta.csv \ ${RDP_SEQS} \ ${RDP_SEQINFO} \ ${USEARCH_HITS} \ ${USEARCH_GROUPS}