Reformat the file names with Perl
#!/usr/bin/perl use strict; use warnings; use File::Copy qw(copy);; $| = 1; my %hash...} } sub read_fh { my $filename = shift @_; my $filehandle; open...2349 days ago
Convert fastq to fasta in Perl
use Bio::SeqIO; #convert .fastq.gz to .fasta open my $zcat, 'zcat seq.fastq.gz |' or die $!; my $in=Bio::SeqIO->new(-fh=>$zcat, -format=>'fastq');...2344 days ago
Insert the sequence at desire location in multi-fasta file with Perl
#!/usr/bin/perl use warnings; use strict; use Bio::SeqIO; use Bio::Seq; use File::Copy...inate should not overlaps --- next postition shold be bigger than firstpos+alienLen open(...2327 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use English; use Pod::Usage; ## uses pod do...-verbose => 0}); } print(STDERR "Loading query sequences into memory..."); open(...2321 days ago
Plot the clock using Lastz -gerenal outfile
use strict; use warnings; use Statistics::R ; use List::Util qw(sum); #Usage perl cl...R->startR ; my $fileN=$ARGV[0]; my $mSize=$ARGV[1]; open (my $fh2, $fileN) or die "Could not open...2312 days ago
Remove duplicate lines with perl
#! perl -sw use strict; my %lines; #open DATA, $ARGV[0] or die "Couldn't open $ARGV[0]: $!\n"; while () { print if not $lines{$_}++; } __DATA__ apple apple plum vinegar apple banana banana banana apple2306 days ago
863 days ago
Plot custom gene density with R
library(karyoploteR) pp2263 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 $...= %$fastaSeq_ref; foreach my $key ( keys %fastaSeq) { open (OUT, ">$outfile") or die "couldn't open...2234 days ago
Perl script to extract the uniq Ids
#!/usr/bin/perl -w use strict; use warnings; use List::Uniq ':all'; open(my $val, "2252 days ago