Perl script to find missing and move to desire folder
#!/usr/bin/perl -w use strict; use warnings; open(my $ids, "2234 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, '2149 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # if the number of input arguments is...[0]; my $filesequence = $ARGV[1]; # open the first file: table of codon usage frequencies if (!open(PROPCODONS,"< $filecodontable...###################################### # open t...2150 days ago
Perl script to count number of Ns in a multifasta file !
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ chomp; next if /^$/; if(/^>/){ $h=substr($_,1); }else{ $n=($_=~tr/nN/nN/);...2139 days ago
Perl subroutine for reading multifasta file !
sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2139 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $| = 1; #Script to...filehandle; if ($filename =~ /gz$/) { open $filehandle, "gunzip -dc $filename |" or die $!; } else { open $...2135 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl for SATSUMA analysis # Us...#Store the ids if ($ARGV[1] eq "ids") { my $idFile="palindrome_ids.txt"; open m...2135 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; # F...### Second, parse the GFF3 my %CDS; my %CDNA; my $mRNA_name; my $frame; open G...2134 days ago
Perl subroutine to read genome/reads fasta file !
sub readSeqFromFasta{ my $file = $_[0]; my (%map,$id,$seq); open(IN,$file) or die("Cannot open file for reading $file:$!\n"); while(){ chomp; if($_ =~ /^>/){ if(defined $id && defined...2128 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, '2120 days ago