[Bioperl-l] a space in Feature key

[Henry Hyun-il Paik]

 Hello Ewan,

 I downloaded data from 

	ftp://ftp.ebi.ac.uk/pub/databases/cpgisle/

 the file name is cpgisle.dat

 - Henry

On Fri, 17 Oct 2003, Ewan Birney wrote:

> 
> 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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