233 days ago
Perl and BioPerl script to extract protein sequences using GFF file !
#!/usr/bin/perl use strict; use warnings; use Bio::DB::Fasta; use Bio::SeqIO; # Paths to your GFF file and genome FASTA file my $gff_file = 'path/to/your/file.gff'; my $gen...233 days ago
Perl script for six frame translation !
...ict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format my...ead the input FASTA file my $seqio = Bio::SeqIO->new(-file =>...frames) { my $translated_seq = translate_frame($sequence,...>translate(-frame => $frame)->seq; } else { # If...233 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(...late() return translated_seq def six_frame_translation(...quence = translate_frame(record.seq, frame) frame_ty...233 days ago
Perl script to calculate the basic stats of the assembled genome !
.../bin/perl use strict; use warnings; use Bio::SeqIO; # Input file containing...ile = 'genome_assembly.fasta'; # Create Bio::SeqIO object to read the FASTA fi...my @contig_lengths; # Iterate through each sequence in the assembly while (...233 days ago
Python script for basic stats of the assembled genome !
from Bio import SeqIO import statistics # Input file containing the genome assembl...0 num_contigs = 0 contig_lengths = [] # Iterate through each sequence in the assembly for record in SeqIO.parse(input_file, 'fasta'):...233 days ago
187 days ago
Python script to calculate basic genome stats !
from Bio import SeqIO def calculate_genome_stats(fasta_fil...g_count = 0 # Read the genome sequence from the FASTA file for record in SeqIO.parse(fasta_file, "fasta"):...sequence.count('G') gc_count += sequence.count('G') + sequence.co...102 days ago
Python script to parse a FASTQ file !
...ct basic information such as the sequence identifier, sequence, and quality scores #pi...nitialize a list to store parsed sequences sequences = []..."id": record.id, "sequence": str(record.seq),...ence']}") print(f"Quality: {seq['quality']}") print()102 days ago