13.figures

#!/bin/bash

source globals

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

per_otus_xls=12.persistent_otus.xls

seq_table=final_otus_sequences
otu_table=final_otus
class_table=final_otus_classifications
blast_table=final_otus_vs_RDP

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

awk -F'\t' -v otu_table="$otu_table" '{ if (line >= 1) { printf("\t\t, SUM(%s) AS \"%s.%s\"\n", $1, $2, $3); } ++line; }' $SAMPLE_INFO_SUBSET >> $SQL

cat << EOF >> $SQL
	FROM $otu_table AS ot
EOF

mysql -h $HOST $DB --local-infile < $SQL > $XLS
sed -i 's/\\t/\t/g' $XLS

samples=`awk '{ if (line > 0) print "O2_" $2; ++line }' $SAMPLE_INFO_SUBSET | sort | uniq`
for sample in $samples
do
	awk -f $0.reshape.awk -v expt="$sample" $per_otus_xls > $0.persistent_otus.reshaped.tab
done

R --no-save < $0.R