[Bioperl-l] (no subject)

[Henry Hyun-il Paik]

 Hello list,

 It is impossible to have a space in Feature key, Right?

 I downlaoded some data from embl cpgisle. They look like below.

---------------------------------------------------------------------------
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.