Downloading mmseqs databases !
# mmseqs databases Usage: mmseqs databases [options] Name Type Taxonomy Url - UniRef100 Aminoacid yes https://www.uniprot.org/he...986 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_all_sampl...931 days ago
Perl script to rename the fasta file !
#Script #1 #!/usr/bin/perl -w use strict; #USAGE #perl extractPattern.pl kmerfasta > uniref100_result_broad my %kHash; local $/ = '>'; my $infile2 = "$ARGV[0]"; # Kmer fasta open( FH2, '902 days ago
Commands to get the detail of disk usage on Linux !
#A simplistic approach would be du -shc /home/* du -shc /home/jnarayan #To sort it: du -smc /home/* | sort -n #There is also a wellknown Perl script that has the option of mailing disk usage reports per user: durep http://www.ubuntugeek.com/create-disk-usage-reports-with-durep.html859 days ago
Command line to print disk usage on Linux terminal !
#Print disk usage - perl du -h |perl -e'%h=map{/.\s/;99**(ord$&&7)-$`,$_}`du -h`;die@h{sort%h}' #Bash du -k * | sort -nr | cut -f2 | xargs -d '\n' du -sh #Base du -scBM | sort -n #More du -s * | sort -rn | cut -f2- | xargs -d "\n" du -sh858 days ago
Perl script to find edit distance between two sequences !
#!/usr/bin/perl use strict; use warnings; sub edit_distance { my ($s1, $s2) = @_; my $len1 = length($s1); my $len2 = length($s2); my @dp; for (my $i = 0; $i469 days ago
Raku script to find palindrome in genomes !
...is-palindrome($substring) { say "Palindrome found at position $pos: $substring"; } } } } # Example usage my $dna = "GGATCCATGGCCTAGG"...469 days ago
Perl script for chi-squared test !
...# Last updated by: $Author$ # Last updated on: $Date$ use strict; use warnings; use Getopt::Long; use FAlite; # sanity checks die "Usage: chidi.pl \n" if (!$ARGV[1])...455 days ago
343 days ago
Perl script to calculate GC content !
...[GC]/g; my $total_bases = length($sequence); my $gc_content = ($gc_count / $total_bases) * 100; return $gc_content; } # Example usage: my $dna_sequence = "ATGCGCT...140 days ago