Read a tab delimited file and search with perl
use strict; use warnings; use Data::Dumper; use Text::CSV; use IO::Handle; my $file = "/home/urbe/Tools/Alienomics_v0.1/Alienomics/output/intermediate_files/rRNA/refGene.megablast"; open my $fh, "[0]\n"; warn Dumper $row; # To see the structure }2540 days ago
Extract fasta sequence from a multifasta file with fasta header Ids
#!/usr/bin/perl use strict; use warnings; #Usage: perl my $list = shift @ARGV; my $fasta = shift @ARGV; my $out = shift @ARGV; my %select; open LIST, "$...2533 days ago
2528 days ago
Calculate Dinucleotide Frequency with Perl
#!/usr/bin/perl -w use strict; my ($genome, $head, $tail); my (%mono_nt, %di_nt); $/ = ">"; open my $fasta, '2353 days ago
Count the number of N in fasta file with Perl
#!/usr/bin/perl my ($h, $n, $l); open(I,$ARGV[0]) or die($!); while(){ chomp; if(/^>/){ $h=substr($_,1); }else{ $n=($_=~tr/nN/nN/); $l=length($_); print $h,"\t",$l,"\t",$n,"\t",$n/($l-$n),"\n"; } } close(I);2481 days ago
Extract the fastq sequence with range in Perl
use Bio::DB::Fasta; open(POSITIONS,"positions.txt"); while(){ chomp; my ($seqName,$begin,$end) = split(/\s/); my $db = Bio::DB::Fasta->new('allGenomeContacted.fa'); my $seq = $db->seq("$seqName", $begin => $end); print "$seq\n"; } close(POSITIONS);2484 days ago
Collision free write with Perl
#Write into outfile -- collision free because of multicore usesage sub collision_free_write { my($outFile, $msg) = @_; open my $ofh, ">>", $outFile or die "$0 [$...2476 days ago
Convert newline formated sequence into fasta format with perl
use strict; use warnings; my $filename = $ARGV[0]; open(my $fh, '2385 days ago
Reformat the file names with Perl
#!/usr/bin/perl use strict; use warnings; use File::Copy qw(copy);; $| = 1; my %hash; my @files = glob "*.scf"; if (!$ARGV[0]){ print "Table file needed\n US...2351 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=>'fast...2346 days ago