[Bioperl-l] problem about format convertion

Chris Fields cjfields at illinois.edu
Sat Mar 14 10:08:47 EDT 2009


Just to note, the Bio::Assembly modules aren't really geared towards  
using Solexa data as far as I know (and there is the problem of the  
ulimit bug that still isn't fixed).

There is interest in getting them up-to-speed but it needs someone  
with the time to do it.

chris

On Mar 14, 2009, at 7:52 AM, Dave Messina wrote:

> 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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