Extract a random sequence from a file
...utfile = 'randomoutput.txt'; open my $in_fh, '', $outputfile; my $size = 21; my $count =...ome = length $genome; my @start_points = shuffle(0 .. $len_genome-$size); next unless @start_poin...2912 days ago
2908 days ago
Perl script to extract fasta sequence by matching name/ids !!
...; while () { chomp; next if /^\s*$/; s/>//g; my @ids=split (/\t/, $_); $select{$ids[0]} = 1; } my $size = keys %select; print "Total Ids $size\n"; close LINE; $/ = "\n>...2873 days ago
Perl script introduces control structures, arrays and hashes.
...'AUGC'); print $first_array[0], "\n\n"; # Scalar gives actual size of an array my $size_of_array = scalar(@first_arra...print "Scalar of array: $size_of_array\n\n"; print "Perl's index size of array: $#first_array\n\n";...2860 days ago
2691 days ago
Genetic Algorithms demonstration with word DNA in Perl
...ulation = shift @_; my $pop_size = scalar @$population; # p...in trouble die "Population size $pop_size is too small" if $p...rent_population[int(rand($pop_size))]; my $child = { survived...ref; printf "generation %d: size %dnleast fit DNA [%s]/%d\n...2369 days ago
2262 days ago
Plot custom gene density with R
library(karyoploteR) pp2247 days ago
Estimate Genome Size with Jellyfish and R
...he run. eg: 1,2,3,..etc. #-C -both-strands Count both strands #-m -mer-len=unit32 Length of the k-mer #-s -size=unit32 Hash size / memory allocation #-o...2244 days ago
Perl script to run SATSUMA in loop !
...dAdinetaV2.fa"; #Ur target file my $satsumaLoc="/home/urbe/Tools/SATSUMA/satsuma-code-0"; # Location of ur SATSUMA my $maxSize = 5000; my $resolution = 5000; my $dotsize = 1; my $cpu=40; my @ids;...2138 days ago