in reply to A strange error message with Bio::SeqIO

You were missing a few things. Here's the code as I think it should be: 
#!/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 input, I took your sequence and put it in a file called seqIOnew.fasta. I tried to get the accession number, but it returned "unknown". Printing out the $seq, you'll see that there is no accession number, so that's why it came back unknown.

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

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And here's the output: 

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]

Replies are listed 'Best First'.
Re^2: A strange error message with Bio::SeqIO
by genbank (Novice) on Aug 26, 2011 at 13:05 UTC

    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.

[reply]
[d/l]
[select]
      You probably didn't use the corrected sequence that I gave you:).
[reply]

        Wow, it's work! I download you sequence and save as 'seq.fasta'. The program not report error message any more and export the expected result. I want to know what the difference bettween the sequences? what I should modify my sequence? Thank you very much!

[reply]

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