122 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::SeqIO; # Paths to your GFF file and genome FASTA file my $gff_file = 'path/to/your/file.g...122 days ago
Perl script for six frame translation !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format my $input_fasta = 'path/to/your/input.fas...122 days ago
Python script for six frame translation of sequences !
from Bio import SeqIO from Bio.Seq import Seq def translate_frame(sequence, frame): if frame > 0: translated_seq = sequence[frame-1:].translate()...122 days ago
Raku script to find repeats in sequences !
sub find-repeats($sequence, $min-repeat-length = 3) { my @repeats; for ^($sequence.chars - $min-repeat-length + 1) -> $i { my $substring = $sequenc...122 days ago
Python script to find repeats in the DNA sequence !
def find_repeats(sequence, min_repeat_length=3): repeats = [] for i in range(len(sequence) - min_repeat_length + 1): substring = sequence[i:i+m...122 days ago
Raku script to find microsatellites in DNA fragments !
sub find-microsatellites($sequence, $min-repeat-length = 2, $max-repeat-length = 6, $min-repeat-count = 3) { my @microsatellites; for my $repeat-length ($mi...122 days ago
Raku script to find overlaps between two bed files !
#!/usr/bin/env raku # Check if the correct number of arguments are provided if @*ARGS.elems != 2 { say "Usage: ./compare_bed_files.raku file1.bed file2.bed";...122 days ago
Perl script to find overlaps between two bed files !
#!/usr/bin/perl use strict; use warnings; # Check if the correct number of arguments are provided if (@ARGV != 2) { die "Usage: $0 file1.bed file2.bed\n"; } # Read the contents of the two BED files my $file1 = shift @ARGV; my $file2 = shift @ARGV; open my $fh1, '122 days ago
Perl script to parse VCF file !
#!/usr/bin/perl use strict; use warnings; # Usage: ./parse_vcf.pl input.vcf die "Usage: ./parse_vcf.pl input.vcf\n" unless @ARGV; my $vcf_file = shift @ARG...122 days ago