[Bioperl-l] Bioperl sim4 parse

Jason Stajich jason at bioperl.org
Fri Oct 1 17:17:36 EDT 2010


Jianmin -

Your question is better addressed to the mailing list bioperl-l at bioperl.org

Please attach an example file that is attached and sample perl code you 
are using so someone can test that your problem exists with the latest code.

-jason

Wang, Jianmin wrote, On 10/1/10 1:59 PM:
> Hi, Jason and Steve,
>
> I checked the code of the sim4.pm and used it in my program.  Unforturnately, it does not work well.  When there is a single hit with a single hsp, the code does not generate the hsp correctly and many of the information are lost.  Could you help me to check the code.  For following is the sim4 output file:
>
> Warning: lowercase letter in d.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (HWI-EAS90_614M9:2:106:16121:11311#0), 12 bp
>
>> chr18:60413870-60414073
>> HWI-EAS90_614M9:2:106:16121:11311#0
>
> 111-122  (1-12)   100%
>
>        0     .    :
>      111 CTCATATAGCTC
>          ||||||||||||
>        1 CTCATATAGCTC
>
> Warning: lowercase letter in q.fa data. Convert sequence to uppercase.
>
> seq1 = d.fa, 203 bp
> seq2 = q.fa (teat), 15 bp
>
>> chr18:60413870-60414073
>> teat
>
> 126-140  (1-15)   100%
>
>        0     .    :    .
>      126 GTGGTATACAGAGTT
>          |||||||||||||||
>        1 GTGGTATACAGAGTT
>
>
>
> I found it's impossible to get the strand and mapping position from the data.
>
> Best.
> Jianmin Wang
>
>
>
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-- 
Jason Stajich
jason at bioperl.org



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