diff usearch-wrapper.sh @ 0:d4690e65afcd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/usearch-wrapper.sh	Thu Feb 26 18:16:36 2015 -0500
@@ -0,0 +1,28 @@
+#!/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}