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";...233 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, '233 days ago
Perl script to calculate the basic stats of the assembled genome !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Input file containing the genome assembly in FASTA format my $input_file = 'genome_assembly.fasta';...233 days ago
Python script to convert fastq to fasta
def fastq_to_fasta(fastq_file, fasta_file): with open(fastq_file, 'r') as fq: with open(fasta_file, 'w') as fa: while True: #...177 days ago
Python script to calculate basic genome stats !
from Bio import SeqIO def calculate_genome_stats(fasta_file): # Initialize variables to store genome statistics genome_length = 0 gc_count = 0 a_c...102 days ago
Python script to parse a FASTQ file !
#Python script to parse a FASTQ file and extract basic information such as the sequence identifier, sequence, and quality scores #pip install biopython from Bio impo...102 days ago