Hi all, I want to use Bio::Tools::Run::Tmhmm to analysis the protein seqence. Firstly, I should feed it the fasta file with Bio::SeqIO. However, the Bio::SeqIO module seem not work and report error as following.

------------- EXCEPTION: Bio::Root::Exception -------------

MSG: The sequence does not appear to be FASTA format (lacks a descriptor line '>')

STACK: Error::throw

STACK: Bio::Root::Root::throw /localperl/lib/site_perl/5.12.4/Bio/Root/Root.pm:368

STACK: Bio::SeqIO::fasta::next_seq /localperl/lib/site_perl/5.12.4/Bio/SeqIO/fasta.pm:127

STACK: tmhmm.pl:6

-----------------------------------------------------------

The code is :

#!/localperl/bin/perl
use strict;
use warnings;
use Bio::SeqIO;
my $inseq = Bio::SeqIO->new(-file   => '/home/zhaoy/document/perl/lwp/
+seq.txt',-format => 'FASTA' ) or die "can't open";
while (my $seq = $inseq->next_seq()) {
 print $seq->accession_number,"\n";
}

[download]

The error message says The sequence does not appear to be FASTA format (lacks a descriptor line '>'),but i am sure all the seqence begin with ">". All the seqences like the seqence as follow:

>gi|1786958|gb|AAC73831.1| membrane spanning protein in TolA-TolQ-TolR complex Escherichia coli str. K-12 substr. MG1655 MTDMNILDLFLKASLLVKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELSRLYQESQ GKRDNLTGSEQIFYSGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELENLETHIPFLGTVGSISPYI GLFGTVWGIMHAFIALGAVKQATLQMVAPGIAEALIATAIGLFAAIPAVMAYNRLNQRVNKLELNYDNFM EEFTAILHRQAFTVSESNKG

I don't know what is wrong with this code. Thanks in advance!

In reply to A strange error message with Bio::SeqIO by genbank

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