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, '107 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...107 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...107 days ago
Python script to parse GFF file
def parse_gff(gff_file): features = [] with open(gff_file, 'r') as f:...omment lines fields = line.strip().split('\t') featur...ds[7], 'attributes': dict(item.split...51 days ago
Python script to finds extact similar sequence between two multi fasta files !
from Bio.Blast.Applications import NcbiblastnCommandline import os import sys def perform_local_blast(query_fi..._handle: for line in result_handle: fields = line.strip().split...16 days ago