2702 days ago
2691 days ago
Perl script to remove the duplicate sequences from multifasta file
use strict; use Bio::SeqIO; my %unique; my $file = "myseqs.fa"; my $seqio = Bio::SeqIO->new(-file => $file, -format => "fasta"); my $outseq = Bio::SeqIO->new(-...2688 days ago
Calculate ATGC percentage in parallel with perl
...qIO; #usage: perl testParallel.pl my %sequences; my $seqio = Bio::SeqIO->new...eq; # and there's your value $sequences{$id} = $seq; } my $max_...sub checkATCG { my $name=shift; my $DNA=$sequences{$name}; my $length=length $D...2654 days ago
Extracting FASTA sequences based on position with perl script !!
#!/usr/bin/env perl #Uses: perl sub-seq.pl input.txt range use strict; use warnings; my $end = pop; my $start = pop; local $/ = '>'; while () {...2620 days ago
Extract fasta sequence from a multifasta file with coordinates
...ath/to/fasta/files/'); while (my $seq = ) { # Bio::PrimarySeqI stuff } # Tied hash access tie %sequences,'Bio::DB::Fasta','/path/to/fasta/files/'; print $sequences{'CHROMOSOME_I:1,20000'};2530 days ago
Create genome scaffolding with Perl
...XN-/TGCAARYSWKMHBDVXN-/; # work on masked sequences as well $seq =~ tr/acgtuyr...{ "query" => 0, # contig file for query sequences "prefix" => "psl_scaffold...se => 0}); } print(STDERR "Loading query sequences into memory..."); open(my $q...2306 days ago
Perl script to remove fasta sequences in multifasta file with certain length threshold
#!/usr/bin/perl use strict; use warnings; my $minlen = shift or die "Error: `minlen` parameter not provided\n"; { local $/=">"; while() { chomp...2249 days ago
Perl script to read multi fasta sequence one by one
...key}\n"; } sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences; open (IN, "2219 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, '2152 days ago