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'; # Create Bio::SeqIO object to...nt the computed statistics and information print "Genom...114 days ago
Python script for basic stats of the assembled genome !
...tistics # Input file containing the genome assembly in FASTA format input_file = 'genome_assembly.fasta' # Variable...header lines line = line.strip() gc_count += lin...ted statistics and information print("Genome Assembly Statistics:") prin...114 days ago
Python script to convert fastq to fasta
def fastq_to_fasta(fastq_file, fasta_file): with open(fastq_file, 'r...lines from the FASTQ file header = fq.readline().strip() sequence = fq.readline().strip() fq.readlin...59 days ago
Python script to parse GFF file
def parse_gff(gff_file): features = [] with open(gff_file, 'r') as f:...t line.startswith('#'): # Ignore comment lines fields = line.strip().split('\t')...59 days ago
Python script to finds extact similar sequence between two multi fasta files !
from Bio.Blast.Applications import NcbiblastnCommandline import os import sys de...result_handle: for line in result_handle: fields = line.strip().split('\t') qs...23 days ago