Perl script to calculate GC content !
#!/usr/bin/perl sub calculate_gc_content { my ($sequence) = @_; $sequence = uc($sequence); # Convert the sequence to uppercase my $gc_cou...s = length($sequence); my $gc_content = ($gc_count / $total...ontent($dna_sequence); printf "GC content: %.2f%%\n", $gc_conte...159 days ago
Python script to convert Multi-line Fasta to Single-line Fasta
...ilename, 'w') as output_file: current_sequence = "" for li...hen the new header if current_sequence:...# Write the last sequence if current_sequence:...158 days ago
Perl script to convert Multi-line Fasta to Single-line Fasta !
#!/usr/bin/perl use strict; use warnings; sub multi_to_single...le, '', $output_filename or die "Error: Could not open file '$output_filename': $!"; my $current_sequence = ""; w...print $output_file $current_sequence . "\n" if $current_sequence;...158 days ago
Bash script to convert Multi-line Fasta to Single-line Fasta !
...ingle_line.fasta" awk '/^>/ {printf("\n%s\n", $0);next; } { printf("%s", $0);} END {printf("\n");}' "$input_filename" > "$output_filename" echo "Successfully converted $input_fil...158 days ago
Bash script to calculate difference between column !
Space Separated awk '{ $5 = $2 - $4 } 1' inputput.txt > outdiff.txt Or with tab separation: awk 'BEGIN { OFS = "\t" } { $5 = $2 - $4 } 1' inputput.txt > outdiff.txt157 days ago
157 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::S...'path/to/your/genome.fasta'; # Gene ID to extract my $gene_id_to_extract = 'y...ne_id'; # Step 1: Parse GFF file to get gene locations my %gene_locations; o...157 days ago
Perl script for six frame translation !
#!/usr/bin/perl use strict; use warnings; use Bio::Se...IO; # Path to your input nucleotide sequence file in FASTA...ormat => 'fasta'); my $sequence = $seqio->next_seq; # Ste..._seq = translate_frame($sequence, $frame); my $frame_typ...rame is negative, reverse and complement the sequence before...157 days ago
Python script for six frame translation of sequences !
...ort Seq def translate_frame(sequence, frame): if frame > 0: translated_seq = sequence[frame-1:].translate() e...everse_complement = sequence.reverse_complement() translate...e(fasta_file, "fasta")) for record in records: print...157 days ago
Raku script to find repeats in sequences !
sub find-repeats($sequence, $min-repeat-length = 3) { my @repeats; for ^($sequence.chars - $min-repeat-length +...$i { my $substring = $sequence.substr($i, $min-repeat-lengt...# Example usage my $genome-sequence = "ATCGATCGATCGATCG"; my @r...157 days ago