Conditional Statements and Loops

for

Using for loop, we can execute a set of commands for a finite number of times for every item in a list.

Syntax

for VARIABLE in LIST
do
  command1
  command2
done

Example

for query in /cluster/tufts/Yourlab/input/*.fasta
do
    echo "Running BLAST for $query"
    blastn -query $query -db /path/to/database -out ${query%.fasta}_blast_results.txt -outfmt 6
done

while

The command next to while is evaluated. If it is evaluated to be true, then the commands between do and done are executed.

Syntax

while [ condition ]
do
   command1
   command2
   command3
done

Example

#!/bin/bash

# File containing the list of sequence files
file_list="sequence_files.txt"
# Path to the BLAST database
blast_db="/path/to/blast_database"

# Read the list of files line by line
while IFS= read -r sequence_file
do
    # Check if the file exists
    if [ -f "$sequence_file" ]; then
        echo "Processing $sequence_file"
        # Run BLAST on the current sequence file
        blastn -query "$sequence_file" -db "$blast_db" -out "${sequence_file%.fasta}_blast_results.txt" -outfmt 6
        echo "Finished processing $sequence_file"
    else
        echo "File $sequence_file not found"
    fi
done < "$file_list"

echo "All files have been processed."

The content of sequence_files.txt is the name of all of the query fasta files:

sequence1.fasta
sequence2.fasta
sequence3.fasta

if: conditionals in a bash script

In bioinformatics, if statements are used to make conditional decisions in scripts, such as checking whether a file or result already exists before performing data analysis or processing tasks, thus optimizing workflows and avoiding redundant computations.

Syntax

if [ commands ]
then
  [ if-statements ]
elif [commands]
  [ elif-statements ]
else
  [ else-statements ]
fi

Example

#!/bin/bash

# Define the paths for input files and output file
input_bam="/path/to/genomic_data.bam"
output_vcf="/path/to/output_directory/variants.vcf"

# Check if the output VCF file already exists
if [ -f "$output_vcf" ]; then
    echo "Output file $output_vcf already exists. Skipping the variant calling step."
else
    echo "Output file $output_vcf does not exist. Running variant calling."

    # Run the variant calling tool (e.g., bcftools)
    bcftools mpileup -Ou -f /path/to/reference_genome.fasta "$input_bam" | \
    bcftools call -mv -Ov -o "$output_vcf"

    echo "Variant calling complete. Results saved to $output_vcf"
fi

This if statement ensures that the variant calling process is skipped if the output file already exists, preventing unnecessary computations and saving processing time. This approach is useful in bioinformatics workflows where redundant analyses can be avoided by checking for existing results.

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