[Bioperl-l] Errors in my script

[nandini_bn]

Thanks a lot for ur reply. I tried changing the format to a flag. that worked
but I am still getting these errors. Could u help me out with these? Thank u

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not open s.Genbank: No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:359
STACK: Bio::Root::IO::_initialize_io /usr/share/perl5/Bio/Root/IO.pm:310
STACK: Bio::SeqIO::_initialize /usr/share/perl5/Bio/SeqIO.pm:454
STACK: Bio::SeqIO::genbank::_initialize
/usr/share/perl5/Bio/SeqIO/genbank.pm:202
STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:351
STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:377
STACK: Bio::SeqIO::newFh /usr/share/perl5/Bio/SeqIO.pm:398


manni122 wrote:
> 
> 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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