[Bioperl-l] Working with SeqWithQuality

Roy Chaudhuri roy.chaudhuri at gmail.com
Thu Jun 19 11:44:37 EDT 2008

Hi Mick,

I think you want Bio::Tools::Alignment::Trim. There are lots of caveats
in the POD but as I recall it works fine.

Here is a small script I wrote to return contigs over a certain length
and a certain minimum quality (not exactly what you asked for but I'm
sure it could be adapted).

use warnings;
use strict;
use Bio::SeqIO;
use Bio::Tools::Alignment::Trim;
use Getopt::Long;
die "Usage: trimqual fasta_file qual_file -qual 20 -window 10 -min
500\n" unless $ARGV[1];
my $phred=20;
my $window=10;
my $min=500;
GetOptions ('phred|qual=i'=>\$phred,
              'minimum=i'=>\$min) or die "Unrecognised option\n";
my $fasta=Bio::SeqIO->newFh(-file=>$ARGV[0], -format=>'fasta');
my $quality=Bio::SeqIO->newFh(-file=>$ARGV[1], -format=>'qual');
my $out=Bio::SeqIO->newFh(-format=>'fasta');
my $count=0;
while (<$fasta>) {
      my $seq=$_;
      my $qual=<$quality>;
      my $trim=Bio::Tools::Alignment::Trim->new(-phreds=>$phred,
      my ($start,$end) = @{$trim->trim_singlet($seq->seq,
                                               join(' ',@{$qual->qual}),
      next if $end==0;
      my $trimmed_sequence=substr($seq->seq, $start, $end+1-$start);
      my $length=length $trimmed_sequence;
      print STDERR $seq->display_id, ": $start-$end [$length bp]";
      if ($length<$min) {
          print STDERR " - skipped\n";
      } else {
          print STDERR "\n";
      my $trimseq=Bio::Seq->new(-seq=>$trimmed_sequence,
      print $out $trimseq;
print STDERR "\nFinished. $count contigs larger than $min bp. were

Dr. Roy Chaudhuri
Department of Veterinary Medicine
University of Cambridge, U.K.

michael watson (IAH-C) wrote:
> Hi
> I have fasta files and separate quality fasta files.  I understand all
> about constructing a SeqWithQuality object, that's the easy bit, but are
> there no functions for actually manipulating the sequence based on the
> quality values?  For example, trimming the ends where a moving window
> average quality does not go above a certain value, or masking areas with
> low quality?  
> Thanks
> Mick
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