[Bioperl-l] Problem using clustalw.pl
James Wasmuth
james.wasmuth@ed.ac.uk
Thu, 09 Jan 2003 13:26:42 +0000
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
King's Buildings
Edinburgh
EH9 3JT
0131 650 7403