Every differential expression analysis ends with a filtering step: keep the genes whose
adjusted p-value is below a cutoff and whose fold change exceeds some magnitude. Doing that in awk
rather than loading the whole table into R is how you handle files too large to open, and it is the
fastest way to answer a quick question about a results table without leaving the terminal.
Statement
Tab-separated data arrives on standard input. The first line of input is a numeric
threshold. The second line is a header row. Every remaining line is a data row whose third column is
a numeric p-value.
Print the complete data rows — all columns, tab separated, exactly as they appeared — for which the
third column is strictly less than the threshold, preserving input order.
Do not print the header. If no rows pass, print nothing.
Input — read from standard input
| Variable | Type | Description |
|---|---|---|
threshold
line 1
|
float |
The p-value cutoff
0 < threshold <= 1
|
header
line 2
|
str |
The tab-separated header row, which is skipped
exactly 3 columns
|
rows
line 3..n
|
str |
Tab-separated data rows with a numeric third column
0 <= rows <= 1000
|
These variables are already read for you in the starter code on the right.
Output
str the full data rows whose third column is strictly below the threshold, in input order
Sample Cases
0.05
gene logFC pval
TP53 2.5 0.001
BRCA1 -1.2 0.03
EGFR 0.4 0.5
MYC 3.1 0.049
TP53 2.5 0.001
BRCA1 -1.2 0.03
MYC 3.1 0.049
0.01
gene fc p
A 1.0 0.001
B 2.0 0.01
A 1.0 0.001Submit also runs your code against 3 hidden test cases. Hidden inputs are never shown — if one fails you'll get its number and a description of the mismatch, not the data.
Constraints
- Comparison is strictly less than: a row equal to the threshold is excluded
- Rows are printed unchanged, including all their columns and original tab separators
- The header row is never printed
- Scientific notation such as
1e-05may appear in the third column and must compare correctly
Further Reading
read -r thrpulls the threshold off the front of the stream beforeawksees the rest.- Pass the threshold in with
-v t="$thr"soawktreats it as a number. $0holds the entire unmodified line, which is what you want to print.
Judged against GNU Bash 5.1.0.