Plot the clock using Lastz -gerenal outfile
use strict; use warnings; use Statistics::R ; use List::Util qw(sum); #Usage perl clockPlot.pl Palindrome.palfc 1500 my $R = Statistics::R->new() ; $R->start...2309 days ago
Perl script to convert fastq to fasta file
...ge = "perl $0 in.fq out.fa"; my $infile = shift or die $usage; my $outfile = shift or die $usage;...file, -sformat1 => 'fastq', -outseq => $outfile, -osformat...2261 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, '2164 days ago
Perl script to read multi fasta sequence one by one
...use strict; use warnings; #USAGE #perl rohanRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_re...q = %$fastaSeq_ref; foreach my $key ( keys %fastaSeq) { open (OUT, ">$outfile") or die "couldn't open th...2231 days ago
Perl script to find coding regions in DNA sequences
...tion of logs my $r = 0.0; $i=0; while ($i < scalar(@codons)) { $r = $r + log($pcodons{$codons[$i]}) - log(1/64); $i = $i + 1; } printf "%.2f\n",$r; __END__...2165 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...#Usage: perl clustalReads.pl genome.fa > HammingDist.txt #Dependancy: MAFFT my ($refSeq, $SeqIds) = fastafile2hash($ARGV[0]); my $tmpFile="tmpOutfile"; foreach my $chr (@$SeqI...2150 days ago
Perl script to convert GFF 2 FASTA !
...::DB::Fasta; $| = 1; # Flush output my $outfile_cds = Bio::SeqIO->new( -fo...fasta', -file => ">$ARGV[2].cds.fasta" ); my $outfile_pep = Bio::SeqIO->new( -fo...asta', -file => ">$ARGV[2].cdna.fasta" ); my $outfile_gene = Bio::SeqIO->new( -f...2149 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, '2135 days ago
Perl script to find palindromic pattern !
..., $p1-$pals, ($pals+1)*2 ); my $st=$p1-$pals; my $sLen=($pals+1)*2; my $ed=($st+$sLen)-1; print "$st\t$ed\t$sLen\t$val\n"; printf "%s%s at %d\n", ' 'x($p1-$pal...2109 days ago
2109 days ago