[Bioperl-l] Bio::SeqIO bug

[Hilmar Lapp]

Just to confirm, is this using the genbank parser as reader and the 
embl parser as writer? Brian/Michael, has either of you checked already 
whether the value correctly comes out of the genbank reader (i.e., 
writer is at fault), or whether the genbank parser reads it wrong 
already?

My bet is it's the writer, but I can't investigate right now.

(Note BTW that we can't just replace every linebreak with a space; if 
the line is broken after a non-word character (comma, dash, etc) then 
we need to just concatenate.)

	-hilmar

On Wednesday, June 23, 2004, at 05:56  PM, Brian Osborne wrote:

> Hilmar and Michael,
>
> Using the latest code, bioperl-live, the pertinent EMBL product is:
>
> FT		/product="Probablenicotinate-nucleotide-
> FT		dimethylbenzimidazol phosphoribosyltransferase CobT"
>
> You can see that the return has not been replaced by a space, as 
> Michael
> said. However the "p" is no longer missing.
>
> Brian O.
>
> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org
> [mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Hilmar Lapp
> Sent: Wednesday, June 23, 2004 11:23 AM
> To: michael watson (IAH-C)
> Cc: Bioperl
> Subject: Re: [Bioperl-l] Bio::SeqIO bug
>
> This may have been fixed in 1.4.x. Did you try a more recent release?
> -hilmar
>
> On Tuesday, June 22, 2004, at 11:28  AM, michael watson (IAH-C) wrote:
>
>> Hi
>>
>> I am using bioperl 1.2.3 on linux.
>>
>> When converting from GenBank to EMBL for the RefSeq entry NC_002945,
>> the
>> following conversion occurs for CDS 2450558..2451643:
>>
>> /product="Probable
>> nicotinate-nucleotide-dimethylbenzimidazol
>> phosphoribosyltransferase CobT"
>>
>> To
>>
>> FT
>> roduct="Probablenicotinate-nucleotide-dimethylbenzimidazol
>> FT                   phosphoribosyltransferase CobT"
>>
>> Note the missing "p" from the FT entry "product", plus the missing
>> spaces in the product text (presumably because "\n"s have been 
>> removed,
>> but in this case they should be replaced by spaces)
>>
>> Rather odd??
>>
>> Mick
>>
>> _______________________________________________
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>> Bioperl-l at portal.open-bio.org
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>>
>>
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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>
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------