678 days ago
Script to rapid genome clustering based on pairwise ANI
First, create a blast+ database: makeblastdb -in...en' -max_target_seqs 10000 -o -num_threads 32 Note: using the -perc_...qs 10000 -perc_identity 90 -o -num_threads 32 Next, calculate pairwi...ing local alignments between sequence pairs: anicalc.py -i -o Finall...649 days ago
Perl script to read the next line of a file !
my $line = ; while(1) { # keep looping until I say so my $nextLine = ; if ($line =~ m/>/ || !defined $nextLine) { ### Do the stuff } ### Do any other stuff; last unless defined $nextLine; $line = $nextLine; }579 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...439 days ago
Perl script for chi-squared test !
#!/usr/bin/perl # # chidi.pl # # A script to perform a chi-squared test of the di...################################################ # Read sequence file 1 ############...################################################ # Read...425 days ago
313 days ago
108 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...108 days ago
Raku script to find overlaps between two bed files !
#!/usr/bin/env raku # Check if the correct number of arguments are provided if @*ARGS.elems != 2 { say "Usage: ./compare_bed_files.raku file1.bed file2.bed"; exit 1; } # Read...108 days ago
Perl script to find overlaps between two bed files !
#!/usr/bin/perl use strict; use warnings; # Check if the correct number of arguments are provided if (@ARGV != 2) { die "Usage: $0 file1.bed file2.bed\n"; } # Read the contents of the two BED files my $file1 = shift @ARGV; my $file2 = shift @ARGV; open my $fh1, '108 days ago