Perl script to parse VCF file !
...se strict; use warnings; # Usage: ./parse_vcf.pl input.vcf die "Usage: ./parse_vcf.pl input.vcf\n" unless @A..._file = shift @ARGV; my @vcf_entries = parse_vcf($vcf_file); print "Tot...osome_counts{$chromosome}\n"; } sub parse_vcf { my ($file) = @_;...91 days ago
Perl script to parse blast results and plot basic stats !
...use List::Util qw(sum); # Usage: ./parse_blast.pl blast_result.txt die "Usage: ./parse_blast.pl blast_result.txt\n"...le = shift @ARGV; my @blast_entries = parse_blast($blast_file); print...core: $avg_bitscore\n"; sub parse_blast { my ($file) = @_;...91 days ago
Python script for basic stats of the assembled genome !
...mputing statistics total_length = 0 num_contigs = 0 contig_lengths = [] # Iterate through each sequence in the assembly for record in SeqIO.parse(input_file, 'fasta'): le...91 days ago
Python script to parse GFF file
def parse_gff(gff_file): features = [] with open(gff_file, 'r') as f:...ature) return features # Usage example gff_file = 'example.gff' parsed_features = parse_gff(gff_file) for feature in...36 days ago
Python script to finds extact similar sequence between two multi fasta files !
...print("Error running BLAST:") print(stderr) def parse_blast_results(output_file): # Parse BLAST results with open(...cal_blast(query_file, subject_file, output_file) # Parse and print BLAST results...6 hours ago