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\...156 days ago
Perl script to calculate the basic stats of the assembled genome !
...SeqIO; # Input file containing the genome assembly in FASTA format my $input_file = 'genome_assembly.fasta'; # Creat...ed statistics and information print "Genome Assembly Statistics:\n"; p...} } return 0; # Should not reach here } # Subroutin...156 days ago
Python script for basic stats of the assembled genome !
...ort SeqIO import statistics # Input file containing the genome assembly in FASTA format input_file = 'genome_assembly.fasta' # Variab...# Print the computed statistics and information print("Genome Assembly Statistics:") pri...156 days ago
Python script to convert fastq to fasta
...dline() # Skip the '+' line quality = fq.readline().strip() # Check for EOF if not header:...100 days ago
Python script to parse GFF file
def parse_gff(gff_file): features = [] with open(gff_file, 'r') as f: for line in f: if not line.startswith('#'): # Ignore comment lines fields =...100 days ago
Python script to calculate basic genome stats !
...Bio import SeqIO def calculate_genome_stats(fasta_file): # Initialize variables to store genome statistics genome_leng...g_count = 0 # Read the genome sequence from the FASTA fil...ent gc_content = (gc_count / genome_length) * 100 if genome_len...26 days ago
Python script to parse a FASTQ file !
..."fastq"): sequence_info = { "id": record.id, "sequence": str(record.seq), "quality": record.letter_annotations["phred_quality"]...26 days ago