DB generation

gistfile1.sh

#!/bin/bash
mysql -u root allbacteria < gff.sql
mysql -u root allbacteria < accession.sql
awk '{ if ($3=="CDS") print $1"\t"$4"\t"$5"\t"$7"\t"$9}' $1.gff | sed -e 's/ID=.*Name=//' -e 's/;Parent.*$//' > $1.txt
cat $1.txt | mysql -u root allbacteria --local-infile=1  -e "LOAD DATA LOCAL INFILE '/dev/stdin' INTO TABLE gff;"
awk '/^>/ {split($0,a,"|");print a[4],"\t",$1}' $1.fasta | sed 's/>//' > $1.txt2
cat $1.txt2 | mysql -u root allbacteria --local-infile=1  -e "LOAD DATA LOCAL INFILE '/dev/stdin' INTO TABLE accession;"