2104 days ago
Perl script to reverse complement a DNA sequence !
#!/usr/bin/perl -w $DNA = 'ACGGGAGGACGGGAAAATTACTACGG...print "Here is the starting DNA:\n\n"; print "$DNA\n\n"; $revcom = reverse $DNA; $revcom =~ s/A/T/g; $rev...ere is the reverse complement DNA: WRONG:\n\n"; print "$revc...ere is the reverse complement DNA:\n\n"; print "$revcom\n";...2087 days ago
Perl script to count occurrence of a character !
#!/usr/bin/env perl # -*- coding: utf-8 -*- #!/usr/bin/perl use strict; use warnings; my %count_of; while ( ) { my @val = split "\t", $_; #my...1944 days ago
Perl One-Liner to print only non-uppercase letters
#Go through file and only print words that do not have any uppercase letters. perl -ne 'print unless m/[A-Z]/' dna.fa > dnaOnlyLowercase.fa #To lowercase everything perl -pne 'tr/[A-Z]/[a-z]/' dnaUpperCase.fa >dnawithoutuppercase.fa;1427 days ago
1384 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed....=250, mininsert=400, maxinsert=600, gaussian] Writing reference. Executing dna.FastaToChromArrays2 [mixed.fa...1034 days ago
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/Q file using `pysa...1020 days ago
Raku script to find palindrome in genomes !
sub is-palindrome(Str $str) returns Bool {...flip; } sub find-palindromes(Str $dna, Int $min-length, Int $max-le...length -> $length { for 0..^$dna.chars - $length -> $pos {...} } } # Example usage my $dna = "GGATCCATGGCCTAGG"; # examp...469 days ago
Raku script to calculate GC content !
sub calculate-gc-content(Str $sequence) { my $gc-count =...return $gc-count / $total-bases * 100; } my $dna_sequence = "ATGCGCTAAAGCGCGCG...CGCGCGCGC"; my $gc_content = calculate-gc-content($dna_sequence); say "DNA Sequen...156 days ago
138 days ago