[Bioperl-l] bioperl modules

[Chris Fields]

You need to install bioperl-run to get Bio::Tools::Run::Alignment::Clustalw.

chris

On Nov 2, 2010, at 12:29 AM, hanbobio wrote:

> Hi, all.
> I ran the bioperl script on suse10, the perl version was 5.8.7 and bioperl version was 1.6 .  But there were some mistake, the following was the message the linux system feelback:
> 
> liaoy at linux:~/nd-hn> perl nd-hn.pl
> 
> Can't locate Bio/Tools/Run/Alignment/Clustalw.pm in @INC (@INC contains: /usr/lib/perl5/5.8.7/i586-linux-thread-multi/usr/lib/perl5/5.8.7/usr/lib/perl5/site_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/site_perl/5.8.7/usr/lib/perl5/site_perl/usr/lib/perl5/vendor_perl/5.8.7/i586-linux-thread-multi/usr/lib/perl5/vendor_perl/5.8.7 /usr/lib/perl5/vendor_perl .) at nd-hn.pl line 26.
> 
> BEGIN failed--compilation aborted at nd-hn.pl line 26.
> The detail of this script in two ways: the attached file and the following script.
> Would you be kindly to test my script and give me some modification or suggestion?
> I myself tested the script some time ago, and my judge was that: the first part(retrieve sequences from remote genebank) and the third part(get the conservative sequences of the multi- sequences alignment outputfile) were right, and  the second part(using the Clustalw to do the multi- sequences alignment) encountered some problem? What the problem is? How can I correct it?
> Thank you very much for your advice.
> 
> Best regards
> Yusheng Liao 2010-11-02
> 
> # retrive sequence from Genbank
> use strict;
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> my $gb = new Bio::DB::GenBank;
> open(OUT,">HCV-5UTR-2.txt")||die "Can't open the file!";
> my $seqout = new Bio::SeqIO(-fh => \*OUT, -format => 'fasta');
> my $query = Bio::DB::Query::GenBank->new
>    (-query   =>'Hepatitis C virus[Organism] AND genotype=1a and 5 UTR',     
>   -db      => 'nucleotide');
> my $seqio = $gb->get_Stream_by_query($query);
> my $i=0;
> while( defined (my $seq = $seqio->next_seq )) {
> $seqout->write_seq($seq);
> $i++;
> print ".";
> }
> print "$i \n";
> # run multi sequence alignment
> use Bio::Tools::Run::Alignment::Clustalw;
> use Bio::SimpleAlign;
> use Bio::AlignIO::clustalw;
> my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM','output'=>'mdf','outfile'=>'HCV-5UTR-2.aln');
> my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
> my $ktuple = 3;
> $factory->ktuple($ktuple); 
> my $inputfilename = '/home/Tonny/perl-5.10.0/HCV-5UTR-2.txt';
> my $aln = $factory->align($inputfilename);
> my $alignout->write_aln(my $aln);
> 
> my $line;
> my @array=('A','C','G','T','-');
> my @arrayX=('a','c','g','t','-');
> my @arrayA;
> my @arrayB;
> my ($i,$j,$k);
> my (@a, at b);
> my %hash;
> open FILE, "/home/Tonny/perl-5.10.0/HCV-5UTR-2.aln" or die;
> open OUT, ">getAlignHCV-5 UTR-1a.txt" or die;
> open OUTA, ">getConsensusHCV-5 UTR-1a.txt" or die;
> while($line=<FILE>){
>      chomp;
>      if($line=~ /CLUSTAL/){
>            next;
>      }elsif($line=~ /^[A-Za-z0-9]/){
>            @a=split /\s+/,$line;
>            if(defined($hash{$a[0]})){
>                  push @{$hash{$a[0]}}, $line;
>            }else{
>                  ${$hash{$a[0]}}[0]=$line;
>                  push @b,$a[0];
>            }
>       }
> }
> for(my $k=0;$k<=$#{$hash{$a[0]}};$k++){    
>      for(my $l=0;$l<=$#b;$l++){
>            print OUT ${$hash{$b[$l]}}[$k];
>            my $seq=(split /\s+/,${$hash{$b[$l]}}[$k])[1];
>            @arrayA=split //,$seq;
>            for($i=0;$i<=$#arrayA;$i++){
>                  if($arrayA[$i] =~ /A/i){
>                        $arrayB[0][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /C/i){
>                        $arrayB[1][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /G/i){
>                        $arrayB[2][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /T/i){
>                        $arrayB[3][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\./i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>                  if($arrayA[$i] =~ /\-/i){
>                        $arrayB[4][$i]++;
>                        $arrayB[5][$i]++;
>                  }
>            }
>       }
>       for($j=0;$j<=$#arrayA;$j++){
>              my $large=0;my $pos=0;
>              for($i=0;$i<=4;$i++){
>                    $arrayB[$i][$j]=$arrayB[$i][$j]/$arrayB[5][$j];
>                    if($arrayB[$i][$j]>$large){
>                          $large=$arrayB[$i][$j];
>                          $pos=$i;
>                    }
>              }
>                    if($large>0.5){
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]=$array[$pos];
>                    }else{
>                            $arrayB[5][$j]=$large;
>                            $arrayB[6][$j]='N';
>                    }
>       }
>       for($i=0;$i<=5;$i++){
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                    if($arrayB[$i][$j]>0){
>                           printf OUT "%.2f\t",$arrayB[$i][$j];
>                    }else{
>                           print OUT "0\t";
>                    }
>              }
>              print OUT "\n";
>        }
>              for($j=0;$j<=15;$j++){
>                    print OUT " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUT "$arrayB[6][$j]\t";
>              }
>              print OUT "\n";
>              for($j=0;$j<=15;$j++){
>                    print OUTA " ";
>              }
>              for($j=0;$j<=$#arrayA;$j++){
>                      print OUTA "$arrayB[6][$j]";
>              }
>              print OUTA "\n";
>        @arrayB=undef;
> }
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