Perl script to parse blast results and plot basic stats !

LEGE — Thu, 01 Feb 2024 02:11:23 -0600
#!/usr/bin/perl

use strict;
use warnings;
use List::Util qw(sum);

# Usage: ./parse_blast.pl blast_result.txt

die "Usage: ./parse_blast.pl blast_result.txt\n" unless @ARGV;

my $blast_file = shift @ARGV;
my @blast_entries = parse_blast($blast_file);

print "Total entries: ", scalar(@blast_entries), "\n";
print "---------------------------\n";

# Print detailed information for each entry
for my $entry (@blast_entries) {
    print "Query:             ", $entry->{QUERY},         "\n";
    print "Subject:           ", $entry->{SUBJECT},       "\n";
    print "Percent Identity:  ", $entry->{PERCENT_IDENTITY}, "\n";
    print "Alignment Length:  ", $entry->{ALIGNMENT_LENGTH}, "\n";
    print "E-value:           ", $entry->{EVALUE},        "\n";
    print "Bit Score:         ", $entry->{BITSCORE},      "\n";
    print "---------------------------\n";
}

# Calculate additional statistics
my $avg_percent_identity = calculate_average(\@blast_entries, 'PERCENT_IDENTITY');
my $avg_alignment_length = calculate_average(\@blast_entries, 'ALIGNMENT_LENGTH');
my ($min_evalue, $max_evalue, $avg_evalue) = calculate_summary_stats(\@blast_entries, 'EVALUE');
my ($min_bitscore, $max_bitscore, $avg_bitscore) = calculate_summary_stats(\@blast_entries, 'BITSCORE');

# Print summary statistics
print "Average Percent Identity:  $avg_percent_identity\n";
print "Average Alignment Length:  $avg_alignment_length\n";
print "E-value Range:             $min_evalue - $max_evalue\n";
print "Average E-value:           $avg_evalue\n";
print "Bit Score Range:           $min_bitscore - $max_bitscore\n";
print "Average Bit Score:         $avg_bitscore\n";

sub parse_blast {
    my ($file) = @_;

    open my $fh, '<', $file or die "Cannot open file $file: $!\n";

    my @entries;

    while (my $line = <$fh>) {
        next if $line =~ /^\s*$/;  # skip empty lines

        chomp $line;
        my @fields = split /\t/, $line;

        my %entry;
        @entry{qw/QUERY SUBJECT PERCENT_IDENTITY ALIGNMENT_LENGTH EVALUE BITSCORE/} = @fields;

        push @entries, \%entry;
    }

    close $fh;

    return @entries;
}

sub calculate_average {
    my ($entries, $field) = @_;
    my @values = map { $_->{$field} } @$entries;
    return @values ? sum(@values) / @values : 0;
}

sub calculate_summary_stats {
    my ($entries, $field) = @_;
    my @values = map { $_->{$field} } @$entries;

    my $min = @values ? (sort { $a <=> $b } @values)[0] : 0;
    my $max = @values ? (sort { $b <=> $a } @values)[0] : 0;
    my $avg = @values ? sum(@values) / @values : 0;

    return ($min, $max, $avg);
}
BOL: Perl script to parse blast results and plot basic stats !

Perl script to parse blast results and plot basic stats !
