BCH709 Introduction to Bioinformatics: Standard Streams and Redirection

Standard Streams and Redirection

Every command has three data streams: input (stdin), output (stdout), and errors (stderr).

The Three Streams

Step 1: Output Redirection

# Redirect output to file (overwrites)
echo "Hello" > output.txt
cat output.txt

Hello

# Append to file (>>)
echo "World" >> output.txt
cat output.txt

Hello
World

# Redirect errors separately
ls nonexistent 2> errors.txt
cat errors.txt

ls: cannot access 'nonexistent': No such file or directory

# Redirect both stdout and stderr
ls genes.txt nonexistent > all.txt 2>&1
cat all.txt

ls: cannot access 'nonexistent': No such file or directory
genes.txt

Step 2: Input Redirection

# Read input from file
wc -l < genes.txt

5

Step 3: Pipes

Connect commands: output of one becomes input of next.

# Count chr1 genes in our data
cat genes.txt | grep "chr1" | wc -l

2

# Sort by score (column 5), show top 3
sort -k5 -rn genes.txt | head -3

chr2	800	1200	geneD	92.5
chr1	600	900	geneB	78.9
chr1	100	500	geneA	45.2

# Save intermediate result with tee
cat genes.txt | grep "chr1" | tee chr1_genes.txt | wc -l
cat chr1_genes.txt

2
chr1	100	500	geneA	45.2
chr1	600	900	geneB	78.9

Redirection Quick Reference