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1 #!/bin/bash
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2
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3 source $(dirname $0)/util.sh
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4 source $1
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5
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6 RDP_SEQS="/shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/rdp/10_31/tax_filter/filtered/rdp_10_31.filter.fasta"
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7 RDP_SEQINFO="/shared/silo_researcher/Matsen_F/MatsenGrp/micro_refset/rdp/10_31/tax_filter/filtered/rdp_10_31.filter.seq_info.csv"
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8
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9 sqlite3 -csv -header ${CLASS_DB} <<EOF > usearch_meta.csv
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10 SELECT pn.name, CAST(pn.mass AS INT) count, tax_id, tax_name, taxa.rank
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11 FROM multiclass_concat
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12 JOIN taxa USING (tax_id)
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13 JOIN placement_names pn USING (placement_id, name)
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14 WHERE want_rank = 'species';
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15 EOF
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16
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17 romp -v usearch_clusters \
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18 --usearch-quietly \
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19 --query-group tax_id \
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20 --query-duplication count \
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21 --database-name seqname \
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22 --database-group tax_id \
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23 ${INPUT_SEQS} \
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24 usearch_meta.csv \
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25 ${RDP_SEQS} \
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26 ${RDP_SEQINFO} \
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27 ${USEARCH_HITS} \
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28 ${USEARCH_GROUPS}
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