[Bioperl-l] Errors in my script

[manni122]

Hi,
it seems that error comes from your line 

my $conin = Bio::SeqIO->new(-seq => $seqobj,
                       -format => 'txt');

"txt" is not supported by this module. Try something else like "fasta".

Markus


nandini_bn wrote:
> 
> Hi, I have written this script using Bioperl methods but it gives me a lot
> of errors: the script is as follows
> Could u please help me out?  
> Thanks
> 
>  
> #! /usr/bin/perl
> 
> use warnings;
> use strict;
> 
> #Reading in an alignment file in msf format from the command line,
> performing an analysis of the alignment
> #Writing the original alignment in fasta format of sequences selected by
> user
> #Storing the consensus sequence as a new sequence object and it's
> annotation in genebank format
> 
> #loading the necessary packages
> use Bio::Perl;
> use Bio::AlignIO;
> use Bio::Seq;
> use Bio::SeqIO;
> 
> #Reading in of msf file
> my $in = Bio::AlignIO->new(-file => $ARGV[0] ,
>                            -format => 'msf');
> 
> #The threshold value
> my $t = $ARGV[1];
> my $aln = $in -> next_aln();
> 
> #some descriptors
> my $length = $aln->length();
> my $residues = $aln->no_residues();
> my $isflush = $aln->is_flush();
> my $sequence = $aln->no_sequences();
> my $identity = $aln->percentage_identity();
> #Consensus sequence
> my $consensus = $aln->consensus_string($t);
> 
> #Printing the details of the alignment
> print "Length: $length \n";
> print "Number of residues: $residues \n";
> print "Is flush: $isflush \n";
> print "Number of sequences: $sequence \n";
> print "Percentage of identity: $identity \n";
> print "Consensus string: $consensus \n";
> 
> #Writing out the file in fasta format
> my $out = Bio::AlignIO->new(-file => ">$ARGV[2]",
>                            -format => 'fasta');
> 
> $out -> write_aln($aln);
> 
> #All ? in the sequence replaced by a X.
> $consensus =~s/\?/X/g;
> 
> print "\n$consensus\n";
> 
> #Making a sequence object with annotation
> my $seqobj = Bio::PrimarySeq->new( -seq => $consensus,
>                                 -id => $identity,
>                                 -organism => $length,
>                                 -comment => $residues,
>                                 -alphabet => 'protein');
> 
> #Writing the consensus sequence in swissprot format
> my $conin = Bio::SeqIO->new(-seq => $seqobj,
>                        -format => 'txt');
> my $conout = Bio::SeqIO->new(-file => ">$ARGV[3]",
>                        -format => 'Genbank');
> 
>  while ( my $seq = $conin->next_seq() )
>     { 
>       $conout->write_seq($seq); 
>     }
> 
> 
> 
> 
> 
> 
> THE ERRORS ARE
> Bio::SeqIO: txt cannot be found
> Exception 
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Failed to load module Bio::SeqIO::txt. Can't locate Bio/SeqIO/txt.pm
> in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.8.8
> /usr/local/share/perl/5.8.8 /usr/lib/perl5 /usr/share/perl5
> /usr/lib/perl/5.8 /usr/share/perl/5.8 /usr/local/lib/site_perl .) at
> /usr/share/perl5/Bio/Root/Root.pm line 425, <GEN0> line 82.
> 
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:359
> STACK: Bio::Root::Root::_load_module /usr/share/perl5/Bio/Root/Root.pm:427
> STACK: Bio::SeqIO::_load_format_module /usr/share/perl5/Bio/SeqIO.pm:555
> STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:376
> STACK: nb175hw4.pl:60
> -----------------------------------------------------------
> 
> For more information about the SeqIO system please see the SeqIO docs.
> This includes ways of checking for formats at compile time, not run time
> Can't call method "next_seq" on an undefined value at nb175hw4.pl line 65,
> <GEN0> line 82.
> 
> 
> 
> 

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