Count GC Content in nucleotide sequence with Perl
...$id = $_; $id =~ s/^>(.+?)\s.+$/$1/g; print OUT "$id\t"; } else { $seq = $seq . $_; }...lcount > 0) { $gccontent = (100 * $gccount) / $totalcount; } else { $gccontent = 0; }...2934 days ago
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Perl script to insert the DNA string in genome
...w(-seq => $upstream.$seqI.$downstream,-display_id => $seq->primary_id,-alphabet => "dna" ); $seq_out->write_seq($seq_obj); } else{ $seq_out->write_se...2687 days ago
BASH script for SelfBLAST a genome
...T a genome -- Expecting you have blast and samtools installed in your system #Au...atabase for MergedContigs.fasta genome exists" else echo "Thanks for testing...-- MAKE SURE U HAVE ADDED CORRECT NAME" samtools faidx MergedContigs.fasta...2680 days ago
Check overlapping range with Perl
...n range $ranges->[0]:\n", join(", ", @$tests), "\n"; } else { print "range $ranges->[0] is empty\n"; } } else { my $pivot = int((...2655 days ago
Extract ids from file with perl
...); my %idHash; my $lastKey; while () { chomp $_; my @cells = split /\t/, $_; $idHash{$cells[0]}=$.; push @allIds, $cel...en $filehandle, "gunzip -dc $filename |" or die $!; } else { open $filehandle,...2636 days ago