[Bioperl-l] FASTA format check

Zhi-Qiang Ye yezhiqiang at gmail.com
Thu May 22 05:06:25 EDT 2008


Thanks, Edward and Fabian.

The Guess module is for guessing formats of valid input, which is not
my requirement.

As for my testing,

>protein\nAAAAAAAAAAAAAAAAAAAAAAAAAAaaa  ==> fasta

>proteinAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA  ==> fasta

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAaaaa  ==> undefined value

AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA  ==> raw

so, what I need is not this one.


Thanks anyway.
Best wishes!

Zhi-Qiang Ye
2008/5/22 Edward Wijaya <ewijaya at gmail.com>:
> Yes there is. Check this out:
>
> http://search.cpan.org/~birney/bioperl-1.4/Bio/Tools/GuessSeqFormat.pm
>
> - Edward
>
> On Thu, May 22, 2008 at 5:07 PM, Zhi-Qiang Ye <yezhiqiang at gmail.com> wrote:
>> Dear all,
>>
>>      I was looking for a module or library for the check of FASTA
>> format.  I have a program taking FASTA format protein sequence as
>> input.
>> If the user provides invalid input, the program has to check it and
>> output friendly error messeges.  Is there any packages or modules with
>> these functionalities?
>>
>>     Thank you very much!
>>
>> Best Regards!
>> --
>> Zhi-Qiang Ye
>> Ph.D in Bioinformatics
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>


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