Raku script to find overlaps between two bed files !
...re_bed_files.raku file1.bed file2.bed"; exit 1; } # Read the contents of the two BED files my @bed1 = slurp(@*ARGS[0]).lines; my @bed2 = slurp(@*ARGS[1]).lines; # Iterate over each inter...138 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 @AR...138 days ago
Perl script to parse blast results and plot basic stats !
#!/usr/bin/perl use strict; use warnings; use List::Util qw(sum); # Usage: ./parse_blast.pl blast_result.txt die "Usage: ./parse_blast.pl blast_result.txt\n...138 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';...138 days ago
Python script for basic stats of the assembled genome !
...ses = 0 with open(file, 'r') as fh: for line in fh: if line.startswith('>'): continue # Skip header lines line = line.stri...138 days ago
Python script to convert fastq to fasta
...sta_file): with open(fastq_file, 'r') as fq: with open(fasta_file, 'w') as fa: while True: # Read four lines from the FASTQ file...82 days ago
Python script to parse GFF file
..._file): features = [] with open(gff_file, 'r') as f: for line in f: if not line.startswith('#'): # Ignore comment lines fields = lin...82 days ago