[Bioperl-l] fasta format

[Jason Stajich]

you can read the man page from sean Eddy or use it exactly as I showed  
you
sreformat fasta filename > filename.new

you can also use the 1st example which is a bioperl solution.

-jason
On Dec 13, 2009, at 7:02 AM, Jonas Schaer wrote:

> Hi Jason,
> thank you very much for your answer.
> i am sorry to bother u again but i'm afraid i need some help with  
> that because i don't see how to use sreformat?
> i dont get it managed to write a script that works.
>
> thank u again :)
> jonas
>
>
> ----- Original Message ----- From: "Jason Stajich" <jason at bioperl.org>
> To: "Jonas Schaer" <Jonas_Schaer at gmx.de>
> Cc: <bioperl-l at bioperl.org>
> Sent: Tuesday, December 08, 2009 6:44 PM
> Subject: Re: [Bioperl-l] fasta format
>
>
>> you can run
>> sreformat (HMMER) or bp_sreformat.pl script in scripts/utilties (or
>> that is installed when you install the Bioperl scripts)
>> $ bp_sreformat.pl -if fasta -of fasta -i yourfile.fa -o  
>> yournewfile.fa
>> # rename it back
>> $ mv yournewfile.fa yourfile.fa
>>
>> or
>> $ sreformat fasta yourfile.fa > yournewfile.fa
>> $ mv yournewfile.fa yourfile.fa
>>
>>
>> -jason
>> On Dec 8, 2009, at 7:21 AM, Jonas Schaer wrote:
>>
>>> Hi there,
>>> I have a little question concerning bioperl. I have
>>> BioPerl-1.6.1.tar.gz installed and i use the fasta.pm module to read
>>> in some fasta files. first it worked fine, but now i have some
>>> fastafiles in slightly different format (not all lines have the same
>>> length!).
>>>
>>> ------------- EXCEPTION -------------
>>> MSG: Each line of the fasta entry must be the same length except the
>>> last.
>>>   Line above #49 '
>>> ..' is 28 != 101 chars.
>>> STACK Bio::DB::Fasta::calculate_offsets C:/Perl/site/lib/Bio/DB/
>>> Fasta.pm:771
>>> STACK Bio::DB::Fasta::index_file C:/Perl/site/lib/Bio/DB/Fasta.pm: 
>>> 681
>>> STACK Bio::DB::Fasta::new C:/Perl/site/lib/Bio/DB/Fasta.pm:491
>>> STACK Bio::DB::Fasta::newFh C:/Perl/site/lib/Bio/DB/Fasta.pm:513
>>> STACK main::readfasta blast_eval.pm:174
>>> STACK toplevel blast_eval.pm:83
>>> -------------------------------------
>>>
>>> indexing was interrupted, so unlinking test.fasta.index at C:/Perl/
>>> site/lib/Bio/
>>> DB/Fasta.pm line 1054.
>>>
>>>
>>> Is there any way to use these fasta files with diffrent length of
>>> lines with this fasta.pm module or will i have to change the format
>>> of my fasta-files(big databases...) ?
>>>
>>> Thanks in advance for any help!
>>>
>>> Regards, Jonas
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> --
>> Jason Stajich
>> jason.stajich at gmail.com
>> jason at bioperl.org
>
>
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--
Jason Stajich
jason.stajich at gmail.com
jason at bioperl.org