[Bioperl-l] Problem using clustalw.pl

[James Wasmuth]

Hi Giuseppe,

it fails to recognise your sequences as two individual ones as the '>' 
is missing from the header...

eg.
 >A01046.PE1

I've run it with the correct headers and it works...

use Bio::Tools::Run::Alignment::Clustalw;
my $in = $ARGV[0];
my @params = ('ktuple' => 2, 'matrix' => 'BLOSUM', 'outfile' => 'out.aln');
my $factory = Bio::Tools::Run::Alignment::Clustalw->new(@params);
my $aln = $factory->align($in);
print STDERR "$aln\n";


J



Giuseppe Torelli wrote:

>Hi,
>
>I'm trying to align two protein sequences in fasta format
>by using clustalw.pl script in the bioperl/examples directory.
>The version of bioperl is 1.0.1. This is the error:
>------------- EXCEPTION  -------------
>MSG: Bad input data (sequences need an id ) or less than 2 sequences in 
>ARRAY(0x83b5bbc) !
>STACK Bio::Tools::Run::Alignment::Clustalw::align 
>/usr/lib/perl5/site_perl/5.6.1/Bio/Tools/Run/Alignment/Clustalw.pm:501
>STACK main::vary_align_order bioperl-1.0.1/examples/clustalw.pl:145
>STACK toplevel bioperl-1.0.1/examples/clustalw.pl:88
>
>And this is the fasta sequence:
>
>  
>
>>A01046.PE1
>>    
>>
>MWLLLTMASLISVLGTTHGLFGKLHPGSPEVTMNISQMITYWGYPNEEYEVVTEDGYILE
>VNRIPYGKKNSGNTGQRPVVFLQHGLLASATNWISNLPNNSLAFILADAGYDVWLGNSRG
>NTWARRNLYYSPDSVEFWAFSFDEMAKYDLPATIDFIVKKTGQKQLHYVGHSQGTTIGFI
>AFSTNPSLAKRIKTFYALAPVATVKYTKSLINKLRFVPQSLFKFIFGDKIFYPHNFFDQF
>LATEVCSREMLNLLCSNALFIICGFDSKNFNTSRLDVYLSHNPAGTSVQNMFHWTQAVKS
>GKFQAYDWGSPVQNRMHYDQSQPPYYNVTAMNVPIAVWNGGKDLLADPQDVGLLLPKLPN
>LIYHKEIPFYNHLDFIWAMDAPQEVYNDIVSMISEDKK
>  
>
>>A01465.PE1
>>    
>>
>MDAMKRGLCCVLLLCGAVFVSPSQEIHARFRRGARSYQVICRDEKTQMIYQQHQSWLRPV
>LRSNRVEYCWCNSGRAQCHSVPVKSCSEPRCFNGGTCQQALYFSDFVCQCPEGFAGKCCE
>IDTRATCYEDQGISYRGTWSTAESGAECTNWNSSALAQKPYSGRRPDAIRLGLGNHNYCR
>NPDRDSKPWCYVFKAGKYSSEFCSTPACSEGNSDCYFGNGSAYRGTHSLTESGASCLPWN
>SMILIGKVYTAQNPSAQALGLGKHNYCRNPDGDAKPWCHVLKNRRLTWEYCDVPSCSTCG
>LRQYSQPQFRIKGGLFADIASHPWQAAIFAKHRRSPGERFLCGGILISSCWILSAAHCFQ
>ERFPPHHLTVILGRTYRVVPGEEEQKFEVEKYIVHKEFDDDTYDNDIALLQLKSDSSRCA
>QESSVVRTVCLPPADLQLPDWTECELSGYGKHEALSPFYSERLKEAHVRLYPSSRCTSQH
>LLNRTVTDNMLCAGDTRSGGPQANLHDACQGDSGGPLVCLNDGRMTLVGIISWGLGCGQK
>DVPGVYTKVTNYLDWIRDNMRP
>
>What is the problem ?
>  
>

-- 

Nematode Bioinformatics
Blaxter Nematode Genomics Group
Institute of Cell, Animal and Population Biology
Ashworth Labs
University of Edinburgh
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