Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D1018 days ago
Commands to Remove White Space In Text Or String Using Awk And Sed In Linux
text=" ATGGTV AGTGACCTAGAGTGATGA G GGRTTT" echo "$text" | sed 's/ //g' OR echo "$text" | awk '{ gsub(/ /,""); print }' Return: ATGGTVAGTGACCTAGAGTGATGAGGGRTTT e...1012 days ago
Oneliner to convert lower-case to sequence masked with Ns
perl -pe '/^[^>]/ and $_=~ s/[a-z]/N/g' genomic.fna > genomic.N-masked.fna awk '{if(/^[^>]/)gsub(/[a-z]/,"N");print $0}' genomic.fna > genomic.N-masked.fna1007 days ago
Perl script for Smith-Waterman Algorithm
# Smith-Waterman Algorithm # usage statement die "usage: $0 \n" unless @ARGV == 2; # get sequences from command line my ($seq1, $seq2) = @ARGV; # scoring scheme...1006 days ago
1006 days ago
Run Pango on your multifasta file !
#More at https://cov-lineages.org/resources/pangolin/usage.html (base) [jnarayan@hn1 FASTA]$ conda activate pangolin (pangolin) [jnarayan@hn1 FASTA]$ ls Input_for_Cova_...944 days ago
bash script to extract sequence by ids !
Use a Perl one-liner, grep and seqtk subseq to extract the desired fasta sequences: # Create test input: cat > in.fasta BGI_novel_T016313 Solyc03g025570.2.1 TTCAAGTGT...880 days ago
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in -dbtype nucl -out Next, use megablast from blast+ package to perform all-vs-all blastn of sequences: blastn -query -db...692 days ago
Perl script to find inverted repeats !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; use Bio::Tools::Run::RepeatMasker; my $genome_file = "genome.fasta"; # read genome sequence my $seqi...481 days ago
Raku script to find palindrome in genomes !
sub is-palindrome(Str $str) returns Bool { $str.=uc; # convert to uppercase $str.=subst:g/\s+//; # remove any spaces return $str eq $str.flip; } sub find-...481 days ago