[Biococoa-dev] GDE format

[Koen van der Drift]

Hi,

I am now working on moving some more formats from BCReader to  
BCSequenceReader. For the GDE format, I looked on the web, and found  
actually two different possibilities. The first one:

{
name "Short name for sequence"
longname "Long (more descriptive) name for sequence"
sequence-ID "Unique ID number"
creation-date "mm/dd/yy hh:mm:ss"
direction [-1|1]
strandedness [1|2]
type [DNA|RNA||PROTEIN|TEXT|MASK]
offset (-999999,999999)
group-ID (0,999)
creator "Author's name"
descrip "Verbose description"
comments "Lines of comments that can be fairly arbitrary text about a  
sequence. Return characters are allowed, but no internal double  
quotes or brace characters. Remember to close with a double quote"
sequence "gctagctagctagctagctcttagctgtagtcgtagctgatgctagct  
gatgctagctagctagctagctgatcgatgctagctgatcgtagctgacg  
gactgatgctagctagctagctagctgtctagtgtcgtagtgcttattgc"
}


but also:
#sf170-A3

atgggaccagagtctaaagccatgtgtaaagttaacccctctctgcgttactttaaattgtagccat--- 
aa catcaccacc---------------------------------

#br20-B1

atgggatcaaagcctaaagccttgtgtaaagttaaccccactctgtgttactttaaattgcattgatttgaa 
  t------------------------------------ 
aatagtactaacaacaataatagtagtggggtaaa



The second one seems to be what Peter added to BCReader. I am not  
familiar with that format, so just wanted to check which one to use.

cheers,



- Koen.