2701 days ago
2689 days ago
Perl script to remove the duplicate sequences from multifasta file
...while(my $seqs = $seqio->next_seq) { my $id = $seqs->display_id; my $seq = $seqs->seq; unless(exists($unique{$seq})) { $outseq->write_seq($seqs); $unique{$seq...2686 days ago
Perl script to insert the DNA string in genome
...a file (genome file) my $out = $ARGV[1]; # output fasta file my $chr="test"; #insertion chromosome my...ay_id => $seq->primary_id,-alphabet => "dna" ); $seq_out->write_seq($seq_obj); } el...2655 days ago
Calculate ATGC percentage in parallel with perl
...use strict; use Parallel::ForkManager; use Bio::SeqIO; #usage: perl testParallel.pl my %sequence...run_on_start( sub { my ($pid,$ident)=@_; #print "** $ident started, pid: $pid\n"; } );...2652 days ago
BASH script for SelfBLAST a genome
...have blast and samtools installed in your system #Author: Jitendra Narayan #USAGE: ./selfBl...asta genome exists" else echo "Thanks for testing this script $USER; Me cr...echo "Something went wrong $USER - Contact jitendra" fi echo "Doing align...2648 days ago
Extract a range from genome file with perl.
...-format => 'fasta'); while (my $seq = $in->next_seq() ) { $seq->display_id( $seq->display_id() . "_$start_pos-$end_pos" ); $out->write_seq( $seq->trunc($start_pos,...2623 days ago
Calculate some statistics for a DNA alignment with Perl
...'emboss', -file => 't/data/insulin.water'); my $aln = $alignin->ne...=> 'fasta', -file => 't/data/nei_gojobori_test.aln'); my $alnobj = $in-...2646 days ago
Check overlapping range with Perl
...1 + int rand 200 for 1..10000; my @tests = map int rand $ranges[-1], 0..1000000; match (\@ranges, \@tests); sub div { my ($b...} sub match { my ($ranges, $tests) = @_; if (@$ranges =...$lt, $ge) = div($ranges->[$pivot], $tests); match([@{$range...2624 days ago
Transpose the file coordinates and plot dendrogram in R
#Save this as tr.awk { for (i=1; i2614 days ago