[Bioperl-l] problem about format convertion

Dave Messina David.Messina at sbc.su.se
Sat Mar 14 05:46:50 EDT 2009


Hi again,
Please keep replies on the mailing list so everyone can follow and
contribute to the discussion.

It's impossible to tell what the problem is with the information you've
given us.

It could be:
1) The .ace file is empty
2) The .ace file is not named "xp_4.ace"
3) The .ace file is not in ace format
4) Bioperl isn't properly installed
etcetera

I don't have BioPerl installed on my computer at the moment; otherwise you
could send me your input file and I could test it here.

But really the solution is for you to check your assumptions. Use a
debugger.

Find a known valid ace file (there's one in the t/data directory that comes
with BioPerl) -- what happens if you run that through your code?

Think about all of the possible reasons why this may not be working, and
test them.


Dave





On Sat, Mar 14, 2009 at 01:52, 苏斐 <sufei at sjtu.edu.cn> wrote:

>
> hi,
> nothing happened as before. The size of xp.phd is zero.
>
> 2009-03-14
> ------------------------------
>  ------------------------------
> *发件人:* Dave Messina
> *发送时间:* 2009-03-14  01:50:55
> *收件人:* 苏斐
> *抄送:* bioperl-l
> *主题:* Re: [Bioperl-l] problem about format convertion
>  Hi,
> Try:
>
>  #!/bin/perl -w
>> use Bio::SeqIO;
>>
>
>
>> $in = Bio::SeqIO->new ( -file => "xp_4.ace", -format => 'ace');
>> $out = Bio::SeqIO->new (-file => ">xp.phd", -format => 'phd');
>> while( $seq = $in->next_seq())
>> {
>> $out->write_seq($seq);
>> }
>>
>
>
> This is covered in the SeqIO HOWTO<http://www.bioperl.org/wiki/HOWTO:SeqIO>
> .
>
>
> Dave
>



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