Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy; #ARGV[0] should be in following format --- Keep the coordinate sorted...2313 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod document...y $lEnd = $fields[12 + ($longTarget * 4)]; my @sBlStarts = split(/,/, $fields[19 + $shortTarget]); my @lBlStarts = split...2307 days ago
Plot the clock using Lastz -gerenal outfile
use strict; use warnings; use Statistics::R ; use List::Util qw(sum); #Usage per...chomp; next if /^$/; #next if empty my @arr = split("\t", $_); if ($arr[7] eq "...5]-$arr[4]; #next if $len < $mSize; my @chr = split...2298 days ago
2263 days ago
Perl script to remove fasta sequences in multifasta file with certain length threshold
#!/usr/bin/perl use strict; use warnings; my $minlen = shift or die "Error: `minlen` parameter not provided\n...chomp; next unless /\w/; s/>$//gs; my @chunk = split...2250 days ago
Plot custom gene density with R
library(karyoploteR) pp2249 days ago
Perl script to find palindromic regions in DNA sequences
use strict; use warnings; my $pp = qr/(?: (\w) (?1) \g{-1} | \w? )/ix; my $filename = $ARGV[0]; open(my $fh, '2153 days ago
Perl script to check fastq reads qualities !
#!/usr/bin/env perl use strict; use warnings; sub readfq { my ($fh, $aux) = @_; @$aux = [undef, 0] if (!defined(@$aux)); return if ($aux->[1]); if (!def...2153 days ago
2209 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is lower than 2 # return a message showi...e the array @codons to store all of the codons in # the input DNA sequence. To split...2154 days ago