Create genome scaffolding with Perl
...my $sEnd = $fields[12 + ($shortTarget * 4)]; my $lEnd = $fields[12 + ($longTarget * 4)]; my @sBlStarts = split(/,/, $fields[19 + $shortTarget]); my @lBlStarts = split(/,/, $fields[19 + $longTarget...2320 days ago
Plot the clock using Lastz -gerenal outfile
...%pHash; while() { chomp; next if /^$/; #next if empty my @arr = split("\t", $_); if ($arr[7] eq "...) { my $len=$arr[5]-$arr[4]; #next if $len < $mSize; my @chr = split '\_', $arr[1]; $chr[0] =~...2310 days ago
Perl script to remove fasta sequences in multifasta file with certain length threshold
...parameter not provided\n"; { local $/=">"; while() { chomp; next unless /\w/; s/>$//gs; my @chunk = split /\n/; my $header = s...2263 days ago
Plot custom gene density with R
library(karyoploteR) pp2261 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 $fh, '2166 days ago
Perl script to find coding regions in DNA sequences
...[$i]; $i = $i + 1; } $seq = "\U$seq"; # we are going to use the array @codons to store all of the codons in # the input DNA sequence. To split the sequence in segments of l...2167 days ago
Perl script to convert GFF 2 FASTA !
#!/usr/bin/perl use strict; use warnings; use Bio::Seq; use Bio::SeqIO; use Bio::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -form...2150 days ago
Perl subroutine to read genome/reads fasta file !
...$file:$!\n"); while(){ chomp; if($_ =~ /^>/){ if(defined $id && defined $seq){ $map{$id} = $seq; $seq=""; } ($id) = split(' ',$_); $id=~s/>//; }...2145 days ago
2138 days ago
Perl script to merge LastZ overlaps
#!/usr/bin/perl use strict; use warnings; use 5.010; # Filter out the exact/direct overlaps from tab seperated alignment file. (lastz format=general- ready) # Do not inclide header in lastz outfile # USAGE: perl filterOverlaps.pl infile > outfile open my $fh, '2137 days ago