Results for "my"
Bio-Scripts
Perl script for chi-squared test !
...e: chidi.pl \n" if (!$ARGV[1]); my @dinucs = qw (AA AC AG AT CA...eotide frequencies of both files my %file1_ob; my %file2_ob; my...ough each sequence in file 1 while(my $entry = $fasta->nextEntry) {...ls of 'rows' in chi-square table my $total; my $row1; my $row2;...467 days ago
Raku script to calculate GC content !
sub calculate-gc-content(Str $sequence) { my $gc-count = $sequence.comb(//).elems; my $total-bases = $sequence.chars; return $gc-count / $total-bases * 100; } my $dna_sequence = "ATGCGCTAAAGC...168 days ago
Raku script to find SSRs in fastq file !
sub find-ssrs(Str $sequence) { my @ssrs; for 2..$sequenc...peats -> $max-repeat { my $repeat = $sequence.substr($m...t - $min-repeats + 1); my $repeat-length = $max-repeat...ss-fastq-file(Str $filename) { my $fh = open $filename, :r;...168 days ago
Perl script to calculate GC content !
.../usr/bin/perl sub calculate_gc_content { my ($sequence) = @_; $seque...ence); # Convert the sequence to uppercase my $gc_count = () = $sequence =~...; my $total_bases = length($sequence); my $gc_content = ($gc_count / $t...152 days ago
Perl script to convert Multi-line Fasta to Single-line Fasta !
...t; use warnings; sub multi_to_single_line_fasta { my ($input_filename, $output_filename) = @_; open my $input_file, '', $output_file...Error: Could not open file '$output_filename': $!"; my $current_sequence = "";...152 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
...Bio::SeqIO; # Paths to your GFF file and genome FASTA file my $gff_file = 'path/to/your/file.gff'; my $genome_fasta = 'path/to/your...r_gene_id'; # Step 1: Parse GFF file to get gene locations my %gene_locations; open my $gf...150 days ago
Perl script for six frame translation !
...tide sequence file in FASTA format my $input_fasta = 'path/to/your/...Step 1: Read the input FASTA file my $seqio = Bio::SeqIO->new(-fil...p 2: Perform six-frame translation my @frames = (1, 2, 3, -1, -2, -...c frame sub translate_frame { my ($sequence, $frame) = @_;...150 days ago
Raku script to find repeats in sequences !
...epeats($sequence, $min-repeat-length = 3) { my @repeats; for ^($seque...chars - $min-repeat-length + 1) -> $i { my $substring = $sequence.substr...} return @repeats; } # Example usage my $genome-sequence = "ATCGATCGA...150 days ago
Raku script to find microsatellites in DNA fragments !
...-length = 6, $min-repeat-count = 3) { my @microsatellites; for my $repeat-length ($min-repeat-l...min-repeat-count + 1) -> $i { my $substring = $sequence.substr...osatellites.unique; } # Example usage my $genome-sequence = "ATCGATCGA...150 days ago
Raku script to find overlaps between two bed files !
...d"; exit 1; } # Read the contents of the two BED files my @bed1 = slurp(@*ARGS[0]).lines; my @bed2 = slurp(@*ARGS[1]).line...heck for overlaps with intervals in the second BED file for my $line2 (@bed2) { my...150 days ago
