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 showing the error if (scalar(@ARGV) < 2) { print "dnalog...2151 days ago
Biological Sequence handling with Perl !
package Sequence::Generic; # File: Sequence/Generic.pm use strict; use Carp; use overload '""' => 'asString', 'neg' => 'reverse', '.'...2177 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($!)...END__ Note: Convert sequences in oneline first perl -pe '/^>/ ? print "\n" : chomp' scaffolds_backup.fasta > out.fasta perl countN.pl scaff.fa Result...2141 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, "2141 days ago
Perl script to find the distance beetween all the contigs and scaffolds
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; $|...ce beetween all the contigs and scaffolds #Usage: perl clustalReads.pl genome.fa > H...e 0 --thread 40 $tmpFile > MAFFT_out"); #usage: perl clustalRead.pl MAFFT_out...2137 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 # User need to set the reference multifasta file name here my $seqfile=""; my $queryfile =...2137 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( -format =>...2135 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($_ =~ /^...2130 days ago
Install Parrot Virtual Machine !
...it@jit-HP-Pro-3335-MT:~/Downloads/parrot-8.1.0$ perl Configure.pl Parrot Version...you're running this program, you obviously have Perl 5--I'll be pulling some defa...th support..........................yes. auto::perldoc - Is perldoc install...1533 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, '2122 days ago