[Bioperl-l] Getting read position information from an ACE file?

[Chris Fields]

Agreed, and it may spur others to get involved, fix bugs, donate code,  
etc.

chris

On Sep 18, 2009, at 10:11 AM, Mark A. Jensen wrote:

> Dan -- I don't know much about Assembly, so can't help there. But  
> can I  encourage you and perhaps one or two others (steganographic  
> content: fangly) to create a HOWTO stub out of this? Would be  
> excellent-
> cheers MAJ
> ----- Original Message ----- From: "Dan Bolser" <dan.bolser at gmail.com>
> To: "BioPerl List" <bioperl-l at lists.open-bio.org>
> Sent: Friday, September 18, 2009 10:55 AM
> Subject: [Bioperl-l] Getting read position information from an ACE  
> file?
>
>
>> Dear Perl Monkeys,
>> I wrote a little demo script for Bio::Assembly::IO here:
>> http://www.bioperl.org/wiki/Module:Bio::Assembly::IO
>> I would very much appreciate comments, criticisms and corrections on
>> that script (please just edit the wiki). For a newbie its always the
>> same question, am I doing it right?
>> In particular, I read about the 4 possible coordinates of a read in  
>> an
>> assembly. My script only retrieves two (?) of the possible four. How
>> should it be adjusted to print all four coordinates for each read?
>> Additionally, I'm not sure how to distinguish between the trimmed  
>> read
>> vs. the full length read and/or the aligned portion of the read vs.
>> the full length read.
>> What I *really* want is the coordinates of the aligned portion of the
>> read in gapped read and gapped consensus space, along with the  
>> quality
>> trimmed range of the read.
>> The ACE file in question is produced by the gsMapper program, which  
>> is
>> part of Newbler from Roche (454), so it has some small
>> 'peculiarities', but I don't think they are critical for the task at
>> hand.
>> Thanks very much for any hep you can provide on any of the above  
>> issues.
>> Sincerely,
>> Dan.
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