File: example16.sh

package info (click to toggle)
sra-sdk 2.9.3%2Bdfsg-1
  • links: PTS, VCS
  • area: main
  • in suites: buster
  • size: 31,724 kB
  • sloc: ansic: 182,592; cpp: 33,717; sh: 5,385; perl: 4,969; makefile: 4,030; python: 3,560; java: 2,363; yacc: 786; lex: 416; lisp: 77; xml: 54
file content (17 lines) | stat: -rwxr-xr-x 441 bytes parent folder | download | duplicates (5) 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
 
echo "----- read NGS in style: PILEUP -----"

TOOL="vdb-sql"
ACC="SRR341578"

TMPFILE=`mktemp -u`

#create a virtual table named SRC on our accession
echo "create virtual table NGS using ngs( $ACC, style = PILEUP, ref = NC_011748.1 );" >> $TMPFILE

#compose the output from 4 values...
echo "select * from NGS limit 1;" >> $TMPFILE

echo "select POS, DEPTH FROM NGS WHERE DEPTH > 130 GROUP BY POS;" >> $TMPFILE
$TOOL < $TMPFILE

rm $TMPFILE