[Bioperl-l] Trouble with Clustalw

[Chris Fields]

Michael,

No, I meant was what version of clustalw (the actual executable) you  
are using.  This is the bioperl wrapper svn version.

What happens if you enter 'clustalw' on the command line?  Do you get:

  **************************************************************
  ******** CLUSTAL 2.0.11 Multiple Sequence Alignments  ********
  **************************************************************

I think the above version has problems with bioperl, though I can't  
recall exactly what the problems were.

chris

On Aug 6, 2009, at 3:39 PM, Michael Rosen wrote:

> Hi Chris,
> I'm not sure, but I don't think so. I see "Clustalw.pm,v 1.36" at  
> the top of the module being called.
>
> Mike
> On Aug 6, 2009, at 1:25 PM, Chris Fields wrote:
>
>> Michael,
>>
>> Are you using ClustalW 2?  I'm not sure but I don't think the  
>> wrapper has been updated for the latest version (I think parsing  
>> still works, though).
>>
>> chris
>>
>> On Aug 6, 2009, at 2:12 AM, Michael Rosen wrote:
>>
>>> I'm a complete bioperl novice, trying to do Clustalw on some fasta  
>>> files, and am running into trouble:
>>>
>>> ~/454DATA> perl TestClust BlastedReads/A0220B0939all.fasta
>>> Use of uninitialized value in concatenation (.) or string at /usr/ 
>>> pubsw/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/ 
>>> Clustalw.pm line 550.
>>> Use of uninitialized value in concatenation (.) or string at /usr/ 
>>> pubsw/lib/perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/ 
>>> Clustalw.pm line 551.
>>> Can't exec "align": No such file or directory at /usr/pubsw/lib/ 
>>> perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm line 555.
>>>
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: Clustalw call ( align  -infile=/tmp/6g7vpegtdP/tBlfRYOnKf - 
>>> output=gcg   -outfile=/tmp/6g7vpegtdP/4WWjuhKS3p) crashed: -1
>>>
>>> STACK: Error::throw
>>> STACK: Bio::Root::Root::throw /usr/pubsw/lib/perl5/site_perl/5.8.8/ 
>>> Bio/Root/Root.pm:328
>>> STACK: Bio::Tools::Run::Alignment::Clustalw::_run /usr/pubsw/lib/ 
>>> perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm:556
>>> STACK: Bio::Tools::Run::Alignment::Clustalw::align /usr/pubsw/lib/ 
>>> perl5/site_perl/5.8.8/Bio/Tools/Run/Alignment/Clustalw.pm:472
>>> STACK: TestClust:22
>>> -----------------------------------------------------------
>>>
>>> Here's my code:
>>>
>>> #!/usr/bin/perl -w
>>>
>>> use Bio::Perl;
>>> use Bio::AlignIO;
>>> use Bio::Tools::Run::Alignment::Clustalw;
>>> use Bio::SimpleAlign;
>>> use Bio::Seq;
>>> use strict;
>>> use warnings;
>>>
>>> my $factory = Bio::Tools::Run::Alignment::Clustalw->new();
>>> my @seq_array = read_all_sequences($ARGV[0],'fasta');
>>>
>>> for (my $i = 0; $i < @seq_array; $i++){
>>>  (my $seq = $seq_array[$i]->seq()) =~ s/-//g;
>>>  $seq_array[$i]->seq($seq);
>>> }
>>>
>>> write_sequence(">test",'fasta', at seq_array);
>>>
>>> my $seq_array_ref = \@seq_array;
>>> my $aln = $factory->align($seq_array_ref);
>>>
>>> my @align_array = $aln->each_seq();
>>> write_sequence(">testfile",'fasta', at align_array);
>>>
>>>
>>> The loop is just there to take out some gaps that were placed in a  
>>> blast previous to this. The write_sequence call confirms that  
>>> @seq_array is a valid array of Bio:Seq objects at the time align  
>>> calls it. Here's some output in "test":
>>>
>>> >A0220B0939one.1 FV584Q101DEWY9
>>> TAAAGGAGCGGTTCACTTCCCGCAGCCCGGCTACCAAGTATTCATCGAGGGGGCCGGTGC
>>> CACCCGCAACCAGGGAATAGGTGATGAAGCGGAGGTAGTAGCCGATGTCGCGGGCACACT
>>> TGGCCTGAAACACATCGCCGTGGCCCATTTCACCCGGCTGGGTCAAGTAAGGGAACCTCT
>>> TGAACACTTCCTGCACCGCTTCCCGCACCAGGGTTTGCTGATTGTTGGTTAGGACACGGG
>>> CCGCTTCCAGAGAAGCAGCAGCACGCTGGTAACGACCATTCACGGCCTGCAGCTCGCTGG
>>> CATTCAGAAAACGCCCTTGATTGTCAGCGGCAGCAATCGCTTCAGTGATGACGGTTTTCA
>>> CCTTGCAACTCCTAAATTCATCAATTGTGTTGTTAACGAACATTCTGTAGGAAAGGCGGA
>>> CTGGATCTCCACCTGCCTATCAGAAATGAAGGGATCTAACCGATCTAAAAAGGGACGACT
>>> AAGCCAGCTTCGACCCAAAGCTCAAACGATGGCG
>>> >A0220B0939one.2 FV584Q101A4DG7
>>> TCGAGGGGGCCGGTGCCACCCGCAACCAGGGAATAGGTAATGAAGCGGAGGTAGTAGCCG
>>> ATGTCGCGGGCACACTTGGCCTGAAACACATCGCCGTGGCCCATTTCCCCCGGCTGGGTC
>>> AAGTAAGGGAACCTCTTGAACACTTCCTGCACCGCTTCCCGCACCAGGGTTTGCTGATTG
>>> TTGGTTAGGACACGGGCCGCTTCCAGAGAAGCAGCAGCACGCTGGTAACGACCATTCACG
>>> GCCTGCAGCTCGCTGGCATTCAGAAAACGCCCTTGATTGTCAGCGGCAGCAATCGCTTCA
>>> GTGATGACGGTTTTCACCTTGCAACTCCTAAATTCATCAATTGTGTTGTTAACGAACATT
>>> CTGTAGGAAAGGCGGACTGGATCTCCACCTGCCTATTAGAAATGAAGGGATCTAACCGAT
>>> CTAAAAAGGACGACTAAGCCAGCTTCGACCCAAAGCTCAAACGATGGCGGCAGCAGCCTT
>>> ATCGAAGTAGCTGGCCACTTCGCTTTGCAGCG
>>> ...
>>>
>>> Thanks,
>>> Mike
>>>
>>>
>>>
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>>
>