Perl script for chi-squared test !
#!/usr/bin/perl # # chidi.pl # # A script to perform a chi-squared test of the di...################################################ # Read sequence file 1 ############...################################################ # Read seque...466 days ago
355 days ago
149 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.fasta'; # Step 1: Read the i...149 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"; exit 1; } # Read the c...149 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, '149 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 FA...at my $input_file = 'genome_assembly.fasta'; # Create Bio::SeqIO object to read the F...149 days ago
Python script to convert fastq to fasta
def fastq_to_fasta(fastq_file, fasta_file): with open(fastq_file, 'r') as fq:...as fa: while True: # Read four lines from the FASTQ file header = fq.readline()...94 days ago
Python script to calculate basic genome stats !
from Bio import SeqIO def calculate_genome_stats(fasta_file): # Initialize variables to store genome stat...0 a_count = 0 t_count = 0 c_count = 0 g_count = 0 # Read the g...19 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...# Initialize a list to store parsed sequences sequences = [] # Read the s...19 days ago