Command line to download blast database / protein
#download all available nr - protein database as a single file #Database location - NCBI where all databases are available ftp://ftp.ncbi.nlm.nih.gov/blast/db/ https://ftp.ncbi...955 days ago
Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options] Name Type...m.nih.gov/blast/db/FASTA - NT Nucleotide - https://ftp.ncbi.nlm...ttp://bcb.unl.edu/dbCAN2 - Resfinder Nucleotide...954 days ago
Onliner to convert multi line fasta to single line fasta !
#Oneliner to convert awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa > fileres.fa #Then delete the first empty line tail -n +2 fileres.fa > fileout.fa940 days ago
Multiline fasta to single line fasta !
perl -pe '$. > 1 and /^>/ ? print "\n" : chomp' in.fasta > out.fasta807 days ago
Bash script to convert multiline fasta to single line fasta !
#file.fa is multiline fasta awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);} END {printf("\n");}' < file.fa778 days ago
Python script to convert Multi-line Fasta to Single-line Fasta
def multi_to_single_line_fasta(input_filename, output_filename): try: with op...lly converted {input_filename} to {output_filename} in single-lin...ilename}' not found.") # Example usage: # multi_to_single_line_f...107 days ago
Perl script to convert Multi-line Fasta to Single-line Fasta !
#!/usr/bin/perl use strict; use warnings; sub multi_to_single_line_fasta { my ($input_filename, $output_f...converted $input_filename to $output_filename in single-lin...multi_to_single_line_fasta('multi_line.fasta', 'single_line.f...107 days ago
Bash script to convert Multi-line Fasta to Single-line Fasta !
#!/bin/bash input_filename="multi_line.fasta" output_filename="single_line.fasta" awk '/^>/ {printf("\n%s\n", $0);n...me" echo "Successfully converted $input_filename to $output_filename in single-line F...107 days ago
Perl script for six frame translation !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Path to your input nucleotide sequence file in FASTA format my $input_fasta = 'path/to/your/input.fasta'; # Step 1: Read the inpu...106 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:...# Replace 'path/to/your/input.fasta' with the actual path to your input nucleotide se...106 days ago