[BioPython] Bio.SeqIO and files with one record

[Jan Kosinski]

Hi,

Do I understand correctly that the function is to return a record 
instead of a parser? If yes I think it could be useful. parse_single 
sounds good.

Cheers,
Jan Kosinski

> Message: 7
> Date: Tue, 10 Jul 2007 21:03:10 +0100
> From: Peter <biopython at maubp.freeserve.co.uk>
> Subject: [BioPython] Bio.SeqIO and files with one record
> To: biopython at lists.open-bio.org
> Message-ID: <4693E5FE.708 at maubp.freeserve.co.uk>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Biopython people,
>
> I'd like a little feedback on the Bio.SeqIO module - in particular, one 
> situation I think could be improved is when dealing with sequences files 
> which contain a single record - for example a very simple Fasta file, or 
> a chromosome in a GenBank file.
>
> http://www.biopython.org/wiki/SeqIO
>
> The shortest way to get this one record as a SeqRecord object is probably:
>
> from Bio import SeqIO
> record = SeqIO.parse(open("example.gbk"), "genbank").next()
>
> This works, assuming there is at least one record, but will not trigger 
> any error if there was more than one record - something you may want to 
> check.
>
> Do any of you think this situation is common enough to warrant adding 
> another function to Bio.SeqIO to do this for you (raising errors for no 
> records or more than one record).  My suggestions for possible names
> include parse_single, parse_one, parse_sole, parse_individual and mono_parse
>
> One way to do this inline would be:
>
> from Bio import SeqIO
> temp_list = list(SeqIO.parse(open("example.gbk"), "genbank"))
> assert len(temp_list) == 1
> record = temp_list[0]
> del temp_list
>
> Or perhaps:
>
> from Bio import SeqIO
> temp_iter = list(SeqIO.parse(open("example.gbk"), "genbank"))
> record = temp_iter.next()
> try :
>      assert temp_iter.next() is None
> except StopIteration :
>      pass
> del temp_iter
>
> The above code copes with the fact that in general some iterators may 
> signal the end by raising a StopIteration except, or by returning None.
>
> Peter
>
> P.S. Any comments on the Bio.AlignIO ideas I raised back in May 2007?
> http://lists.open-bio.org/pipermail/biopython/2007-May/003472.html
>
>
>
>   

:.