1echo "----- produce FASTQ ( with split-spot !) -----" 2 3TOOL="vdb-sql" 4ACC="SRR341577" 5 6TMPFILE=`mktemp -u` 7 8#create a virtual table named FASTQ on our accession 9echo "create virtual table SRC using vdb( $ACC, " >> $TMPFILE 10echo " columns = SPOT_ID;NAME;READ;(INSDC:quality:text:phred_33)QUALITY;READ_START;READ_LEN );" >> $TMPFILE 11 12#set the separator to new-line 13echo ".separator \"\n\"" >> $TMPFILE 14 15#compose the output from 4 values... 16echo "select" >> $TMPFILE 17 18echo " printf( '@%s.%s %s length=%s', '$ACC', SPOT_ID, NAME, json_extract( READ_LEN, '$.a[0]' ) ), " >> $TMPFILE 19echo " substr( READ, json_extract( READ_START, '$.a[0]' ) + 1, json_extract( READ_LEN, '$.a[0]' ) ), " >> $TMPFILE 20echo " printf( '+%s.%s %s length=%d', '$ACC', SPOT_ID, NAME, json_extract( READ_LEN, '$.a[0]' ) ), " >> $TMPFILE 21echo " substr( QUALITY, json_extract( READ_START, '$.a[0]' ) + 1, json_extract( READ_LEN, '$.a[0]' ) ), " >> $TMPFILE 22echo " printf( '@%s.%s %s length=%s', '$ACC', SPOT_ID, NAME, json_extract( READ_LEN, '$.a[1]' ) ), " >> $TMPFILE 23echo " substr( READ, json_extract( READ_START, '$.a[1]' ) + 1, json_extract( READ_LEN, '$.a[1]' ) ), " >> $TMPFILE 24echo " printf( '+%s.%s %s length=%d', '$ACC', SPOT_ID, NAME, json_extract( READ_LEN, '$.a[1]' ) ), " >> $TMPFILE 25echo " substr( QUALITY, json_extract( READ_START, '$.a[1]' ) + 1, json_extract( READ_LEN, '$.a[1]' ) ) " >> $TMPFILE 26 27echo "from SRC LIMIT 12;" >> $TMPFILE 28 29$TOOL < $TMPFILE 30 31rm $TMPFILE 32