137 days ago
Python script for six frame translation of sequences !
from Bio import SeqIO from Bio.Seq import Seq def translate_frame(sequence, frame): if frame > 0: translated_seq = sequence[frame-1:].translate()...137 days ago
Python script to find repeats in the DNA sequence !
def find_repeats(sequence, min_repeat_length=3): repeats = [] for i in range(len(sequence) - min_repeat_length + 1): substring = sequence[i:i+m...137 days ago
Python script for basic stats of the assembled genome !
from Bio import SeqIO import statistics # Input file containing the genome assembly in FASTA format input_file = 'genome_assembly.fasta' # Variables for computi...137 days ago
Python script to convert fastq to fasta
def fastq_to_fasta(fastq_file, fasta_file): with open(fastq_file, 'r') as fq: with open(fasta_file, 'w') as fa: while True:...81 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 line...81 days ago
Python script to finds extact similar sequence between two multi fasta files !
...uery Sequence:", qseq) # Print other relevant information if needed def main(): if len(sys.argv) != 4: print("Usage: python script.py query.fasta subject...46 days ago
34 days ago
Python script to create fastq file with random sequences
import random def generate_random_sequence(length): bases = ['A', 'C', 'G', 'T'] return ''.join(random.choice(bases) for _ in range(length)) def generat...6 days ago
Python script to calculate basic genome stats !
from Bio import SeqIO def calculate_genome_stats(fasta_file): # Initialize variables to store genome statistics genome_length = 0 gc_count = 0 a_...6 days ago