genbank:

You're sure that all sequences are fasta format, and it's sure that at least one isn't. You need to *prove* it one way or the other. I'd suggest printing out the line number or something as you process through the file so you can find out where in your file it's having trouble. Then double and/or triple check the input.

Also, take the error message with a grain of salt: Sometimes an error isn't exactly what's claimed. For example, if a descriptor line requires four vertical bars, the record might not be recognized as a descriptor line and generate such a message.

NOTE: I've never used the Bio::SeqIO module (nor any of the other bio modules), so take my advice with a grain of salt. I'm just speaking from experience with other things.

...roboticus

When your only tool is a hammer, all problems look like your thumb.

#!/usr/bin/perl 

use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new(
          -file   =>  "/root/Desktop/seqIOnew.fasta",
          -format => 'FASTA');
my $out = Bio::SeqIO->new(
          -file   => ">/root/Desktop/new_out.log",
          -format => "EMBL" );                       
while ( my $seq = $in->next_seq() ) {
        print $out->write_seq($seq), "\n";
}
[download]

For the output, I used new_out.log on my desktop.

Here's the corrected sequence:

>gi|1786958|gb|AAC73831.1| membrane spanning protein in TolA-TolQ-TolR
+ complex [Escherichia coli str. K-12 substr. MG1655] MTDMNILDLFLKASLL
+VKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELSRLYQESQ GKRDNLTGSEQIFY
+SGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELENLETHIPFLGTVGSISPYI GLFGTVWGIMHA
+FIALGAVKQATLQMVAPGIAEALIATAIGLFAAIPAVMAYNRLNQRVNKLELNYDNFM EEFTAILHRQ
+AFTVSESNKG
[download]

ID   unknown; SV 1; linear; ; STD; UNC; 0 BP.
XX
AC   unknown;
XX
DE   membrane spanning protein in TolA-TolQ-TolR complex [Escherichia 
+coli str.
DE   K-12 substr. MG1655]
DE   MTDMNILDLFLKASLLVKLIMLILIGFSIASWAIIIQRTRILNAAAREAEAFEDKFWSGIELSRL
+YQESQ
DE   GKRDNLTGSEQIFYSGFKEFVRLHRANSHAPEAVVEGASRAMRISMNRELENLETHIPFLGTVGS
+ISPYI
DE   GLFGTVWGIMHAFIALGAVKQATLQMVAPGIAEALIATAIGLFAAIPAVMAYNRLNQRVNKLELN
+YDNFM
DE   EEFTAILHRQAFTVSESNKG
XX
FH   Key             Location/Qualifiers
FH
XX
//
[download]

Hi Khen1950fx, thank you for your help. I have copyed you code, and run on my computer(just change the path of the file). However I get the same error message, "the sequence does not to be FASTA format(lacks a descriptor line '>')". The code I run as following:

#!/localperl/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new(
          -file   =>  "/home/zhaoy/document/perl/lwp/seq.fasta",
          -format => 'FASTA');
my $out = Bio::SeqIO->new(
          -file   => ">/home/zhaoy/document/perl/lwp/new_out.log",
          -format => "EMBL" );
while ( my $seq = $in->next_seq() ) {
        print $out->write_seq($seq), "\n";
}
[download]

I receive the error message:

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: The sequence does not appear to be FASTA format (lacks a descript
+or 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:12
-----------------------------------------------------------
[download]

The same program, gain different results. Maybe the problem is that the installation of bioperl. But I am not sure.

You probably didn't use the corrected sequence that I gave you:).

Sounds like you have a corrupt fasta file. Try running this against it:

perl -nlE"/^>/ or /^[A-Z]+$/ or say 'Bad FASTA at ', $." theFile.fasta
[download]