[Bioperl-l] Problems with EMBL entries and fasta IDs?

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Tue Dec 19 07:20:56 EST 2006


Hi

I'm using bioperl-1.4.  I did do a google search fro this but couldn't
find anything.  If this is fixed in 1.5.2 then forgive me.

I'm getting a warning:

MSG: No whitespace allowed in FASTA ID [unknown id]

When trying to convert from EMBL format to fasta.  The offending
sequence is CK234114:

ID   CK234114; SV 1; linear; mRNA; EST; VRT; 244 BP.
XX
AC   CK234114;
XX
DT   03-MAR-2004 (Rel. 79, Created)
DT   03-MAR-2004 (Rel. 79, Last updated, Version 1)
XX
DE   SB010002000A01 JUWNL1 Normalized Zebra Finch Juvenile Telencephalon
cDNA
DE   Library SB01 Taeniopygia guttata cDNA clone SB010002000A01 5', mRNA
DE   sequence.
Etc

Any advice?

Mick

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