4.3.read_count

#!/bin/bash

SQL=$0.read_sums.sql
XLS=$0.read_sums.xls

AB=otu_table_non_chimeric_rdp.tab

otu_table=master_otu_table

cat << EOF > $SQL
.mode tabs
SELECT ot.OTUId
EOF

head -2 $AB | tail -1 | awk -F'\t' -v frac_cutoff=$FRAC_CUTOFF '{ for (i = 2; i <= NF; ++i) { printf("\t\t, SUM(%s) AS %s\n", $i, $i); } }' >> $SQL

cat << EOF >> $SQL
	FROM $otu_table AS ot
	WHERE domain <> "Archaea"
;
EOF

sqlite3 -header database.sqlite3 < $SQL > $XLS

#awk -f $0.reshape.awk -v expt="H1" 44.master_otu_table.no_Archaea.0.01.xls > $0.persistent_otus.reshaped.tab
#awk -f $0.reshape.awk -v expt="L1" 44.master_otu_table.no_Archaea.0.01.xls >> $0.persistent_otus.reshaped.tab

R --no-save < $0.R