[Bioperl-l] (no subject)

[Ewan Birney]

On Friday, October 17, 2003, at 07:15  pm, Henry Hyun-il Paik wrote:

>
>  Hello list,
>
>  It is impossible to have a space in Feature key, Right?
>
>  I downlaoded some data from embl cpgisle. They look like below.
>

I don't think you are allowed spaces. Where did you get this from?



> ----------------------------------------------------------------------- 
> ----
> ID   GAPDHG
> AC   J04038;
> LE   5378
> DE   Human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene,  
> complete
> cds.
> DE   7/95
> EX   Gene expression widespread
> FT   CpG island      871..1673
> FT                   /size=803
> FT                   /%(C+G)=69.12
> FT                   /Obs/Exp CpG=0.82
> FT   CpG island      1683..2063
> FT                   /size=381
> FT                   /%(C+G)=67.19
> FT                   /Obs/Exp CpG=0.77
> XX
> FT                   /CAAT-box.1="884"
> FT                   /CAAT-box.2_complement="2156"
> FT                   /GC-box="1064"
> FT                   /E2F_CS.1="1785"
> FT                   /SpI="158,1198,1244,1290,1310,1314"
> FT                   /SpI_complement="174,584,1519,1668,1736,2271"
> FT                   /SpI_complement="2625"
> FT                   /AccII="717,727,1093,1268,1334,1423"
> FT                   /AccII="1489,1531,1788,2006,3650,4278"
> //
> ----------------------------------------------------------------------- 
> -
>
>  I tried to parse this by using SeqIO. It didn't work.
>
>  I got an error message like below.
>
>   
> -----------------------------------------------------------------------
>
> Argument "island" isn't numeric in numeric gt (>) at
> /home/hy1001/bin/Bio/Location/Atomic.pm line 91, <GEN0> line 15.
> Argument "island" isn't numeric in numeric gt (>) at
> /home/hy1001/bin/Bio/Location/Atomic.pm line 91, <GEN0> line 15.
>
> ------------- EXCEPTION  -------------
> MSG: Got a sequence with no letters in - cannot guess alphabet []
> STACK Bio::PrimarySeq::_guess_alphabet
> /home/hy1001/bin/Bio/PrimarySeq.pm:817
> STACK Bio::PrimarySeq::seq /home/hy1001/bin/Bio/PrimarySeq.pm:276
> STACK Bio::PrimarySeq::new /home/hy1001/bin/Bio/PrimarySeq.pm:214
> STACK Bio::Seq::new /home/hy1001/bin/Bio/Seq.pm:498
> STACK Bio::Seq::RichSeq::new /home/hy1001/bin/Bio/Seq/RichSeq.pm:115
> STACK Bio::Seq::SeqFactory::create
> /home/hy1001/bin/Bio/Seq/SeqFactory.pm:126
> STACK Bio::SeqIO::embl::next_seq /home/hy1001/bin/Bio/SeqIO/embl.pm:344
> STACK toplevel extracted.pl:13
>
>   
> -----------------------------------------------------------------------
>
>  So I changed 'CpG island' to 'CpG_island'. Then it worked fine.
>
>  I am using perl 5.8.0 and bioperl 1.2.3 on linux.
>
>  Thank you.
>
>  - Henry.
>
>
>
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