[Biojava-l] WriteFasta

[Andy Yates]

Is it possible for you to send us the code which you're trying to run & 
the sequence you are trying to write out. If it is sent to us in a 
manner we can drop it into an IDE & run that would help us a lot.

Thanks,

Andy Yates

Saif Ur-Rehman wrote:
> Dear Richard,
> 
> I have tried the RichSEquence.IOTools.writeFasta method and this method is still
> appending the characters "??" to the front of each write. I am using a 
> FileOutputStream and a Sequence object as inputs to the method. like so.
> 
> 
>  Sequence seq; // read in from File
>  FileOutputStream f =new FileOutputStream (fileName);
> 
> 
> 			   try{
> 
> 			    	RichSequence.IOTools.writeFasta(f,
> 			    	        seq,
> 			    	        RichObjectFactory.getDefaultNamespace()
> 			    	        );
> 
> 
> 			    }
> 
> 
> Thanks a lot for your time
> 
> Sincerely,
> 
> Saif
> 
> Quoting Richard Holland <holland at ebi.ac.uk>:
> 
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> SeqIOTools is deprecated.
>>
>> Try RichSequence.IOTools.writeFasta() instead to see if that helps.
>>
>> e.g.:
>>
>> RichSequence.IOTools.writeFasta(
>> 	System.out,
>> 	seq,
>> 	RichObjectFactory.getDefaultNamespace()
>> 	);
>>
>> where seq is either a Sequence or a SequenceIterator.
>>
>> cheers,
>> Richard
>>
>> Saif Ur-Rehman wrote:
>>> Dear All,
>>>
>>> I was writing to ask about the SeqIOTools.writeFasta() Method. I am
>> currently
>>> trying to break up Fasta Files of whole organisms into one file per gene
>> for
>>> further analysis. However the writeFasta method appears to append the
>>> characters
>>> "¨Ì
>>>
>>> ------------------------------------------------------------------
>>> University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
>>>
>>> _______________________________________________
>>> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/biojava-l
>>>
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>> iD8DBQFHBQVe4C5LeMEKA/QRAvBDAKCQkyH+a6TK5VpgfpSmAgfTUPrG+gCgkIJp
>> C4xPs/2ywAMfIPDmUKPCrqg=
>> =TwwH
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>>
> 
> 
> -------------------------------------------------------------------------------
> Saif Ur-Rehman
> Research Student
> The Centre for Evolution, Genes & Genomics (CEGG)
> Dyers Brae
> School of Biology
> The University of St Andrews
> St Andrews,
> Fife
> Scotland,UK
> 
> ------------------------------------------------------------------
> University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
> 
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