We need to print out
targetID="123"
AssayID="456",
awk -F\", 'BEGIN{FS=",";OFS=",";} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$13,$14,$15,$16,$17,$18,$19,$20,$12}' VrtAssay_123_target_456_assay_Detail2.csv > VrtAssay_123_target_456_assay_Detail2_reorder.csv
A. We try:
printf "awk -F"\""," 'BEGIN{FS=\",\";OFS=\",\";} {print \$1,\$2,\$3,\$4,\$5,\$6,\$7,\$8,\$9,\$10,\$11,\$20,\$12,\$13,\$14,\$15,\$16,\$17,\$18,\$19}' VrtAssay_${TargetIDs}_target_${AssayID}_assay_Detail2_average.csv > VrtAssay_${TargetIDs}_target_${AssayID}_assay_Detail3.csv"
B. or echo
echo "awk -F"\"", 'BEGIN{FS=\",\";OFS=\",\";} {print \$1,\$2,\$3,\$4,\$5,\$6,\$7,\$8,\$9,\$10,\$11,\$20,\$12,\$13,\$14,\$15,\$16,\$17,\$18,\$19}' VrtAssay_${TargetIDs}_target_${AssayID}_assay_Detail2_average.csv > VrtAssay_${TargetIDs}_target_${AssayID}_assay_Detail3.csv"
Both give (\ is gone)
awk -F", 'BEGIN{FS=",";OFS=",";} {print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10,$11,$13,$14,$15,$16,$17,$18,$19,$20,$12}' VrtAssay_123_target_456_assay_Detail2.csv > VrtAssay_123_target_456_assay_Detail2_reorder.csv
C. If we try
printf "awk -F\\", 'BEGIN{FS=\",\";OFS=\",\";} {print \$1,\$2,\$3,\$4,\$5,\$6,\$7,\$8,\$9,\$10,\$11,\$20,\$12,\$13,\$14,\$15,\$16,\$17,\$18,\$19}' VrtAssay_${TargetIDs}_target_${AssayID}_assay_Detail2_average.csv > VrtAssay_${TargetIDs}_target_${AssayID}_assay_Detail3.csv"
These will give an error message of
Unmatched ".
D. If we try
echo "awk -F\\", 'BEGIN{FS=\",\";OFS=\",\";} {print \$1,\$2,\$3,\$4,\$5,\$6,\$7,\$8,\$9,\$10,\$11,\$20,\$12,\$13,\$14,\$15,\$16,\$17,\$18,\$19}' VrtAssay_${TargetIDs}_target_${AssayID}_assay_Detail2_average.csv > VrtAssay_${TargetIDs}_target_${AssayID}_assay_Detail3.csv"
This gives us
Unmatched ".
Wonder any guru could kindly offer some solutions?
Any of these work, you just need to make sure that everything's escaped properly:
$ echo 'awk -F\",'
$ echo awk -F\\\",
$ echo "awk -F\\\","
The shell's parsing rules are basically:
'single quotes', everything except for single quotes is interpreted literally; to include a literal single quote, you need to close the single quote and then use double quotes to get that."double quotes", double quotes and backslashes must be escaped with a backslash. So, a literal double quote is \", a literal backslash is \\, and a literal backslash and double quote are \\\". If you just write \\", that's a literal backslash followed by a closing quote.