Reformat the file names with Perl
...trict; use warnings; use File::Copy qw(copy);; $| = 1; my %hash; my @files = glob "*.scf"; if (!$ARGV[0]){ print "Table file needed\n USAGE: $0 table\n"; exit;} my $i...2377 days ago
Create genome scaffolding with Perl
...; use strict; use English; use Pod::Usage; ## uses pod documentation in usage code use Getopt::Long qw(:co...pslFiles, $argument); } else { pod2usage({-exitVal => 1,...es; if(!$projOpts->{"query"}){ pod2usage({-exitVal => 1,...2349 days ago
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->startR ; my $fileN...2340 days ago
Perl script to convert fastq to fasta file
#!/usr/bin/env perl use strict; use warnings; use Bio::Factory::EMBOSS; my $usage = "perl $0 in.fq out.fa"; my $infile = shift or die $usage; my $outfile = shift or die $usage; my $factory = Bio::Fa...2292 days ago
Perl script to read multi fasta sequence one by one
#!/usr/bin/env perl use strict; use warnings; #USAGE #perl rohanRun.pl seq.fa my $outfile='tmp.fa'; my $fastaSeq_ref = readfasta ("$ARGV[0]"); my %fastaSeq = %$fastaSeq_re...2262 days ago
Perl script to find coding regions in DNA sequences
...my $filesequence = $ARGV[1]; # open the first file: table of codon usage frequencies if (!open(PROP...n not be opened\n"; exit(1); } # load the frequencies of codon usage into the hash table %pcodons...2196 days ago
Perl script to find the distance beetween all the contigs and scaffolds
...#Script to see the distance beetween all the contigs and scaffolds #Usage: perl clustalReads.pl genome....mafft --retree 1 --maxiterate 0 --thread 40 $tmpFile > MAFFT_out"); #usage: perl clustalRead.pl MAFFT_ou...2181 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=...2181 days ago
2167 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, '2166 days ago