[Bioperl-l] problem about format convertion

Dave Messina David.Messina at sbc.su.se
Sat Mar 14 08:52:31 EDT 2009


Hi,
I strongly urge you to use another ace file to test whether the problem is
with the code or with your ace file.

I don't know of another ace to phd converter; perhaps google or someone else
on the list can suggest one.

Dave





On Sat, Mar 14, 2009 at 12:25, <sufei at sjtu.edu.cn> wrote:

> hi,
> My ace file is so big to send to you. My data comes from Solexa, so the ace
> file is more than 1.5G. Would you like to tell me another way or other tools
> to convert ace file to phd file?
>
>
>
> Quoting Dave Messina <David.Messina at sbc.su.se>:
>
>  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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