[Bioperl-l] error fetching seqs from a local db on win2k

[Richard Jacob]

Here is the error that the script reports on win2k:

accession number: P31448
------------- EXCEPTION  -------------
MSG: swissprot stream with no ID. Not swissprot in my book
STACK Bio::SeqIO::swiss::next_seq C:/Perl/site/lib/Bio/SeqIO/swiss.pm:155
STACK Bio::Index::AbstractSeq::fetch 
C:/Perl/site/lib/Bio/Index/AbstractSeq.pm:145
STACK toplevel D:\Richard\Dev\xlinker\fetch_from_sprot.pl:15

--------------------------------------
I tried to use the index generated under linux but I belive that it 
incorporates the file path into the index and it, predictably, did not make 
a difference.

I noticed that the *.pap file is very large - bigger than the correct index 
file.
For sprot40 the working index is 10MB
while on windows the .pap file is 32MB.
Finally the .dir file is only 10kb.



>If I then run a script to fetch a sequence I have to use the index name
>of swiss.inx or it fails with errors. Using either of the two files
>names that the indexing generated causes the script to fail straight
>away. When I do use swiss.inx only the first entry can be fetched all
>others fail.
>

Heres the output for the script if I use swiss.idx.pap rather than 
swiss.idx in my script.

accession number: P31448
------------- EXCEPTION  -------------
MSG: Can't open 'SDBM_File' dbm file 'swiss.idx.pap' : No such file or 
directory

STACK Bio::Index::Abstract::open_dbm C:/Perl/site/lib/Bio/Index/Abstract.pm:393
STACK Bio::Index::Abstract::new C:/Perl/site/lib/Bio/Index/Abstract.pm:151
STACK Bio::Index::AbstractSeq::new C:/Perl/site/lib/Bio/Index/AbstractSeq.pm:91
STACK toplevel D:\Richard\Dev\xlinker\fetch_from_sprot.pl:13

--------------------------------------

I belive that the problem is with the indexing of databases on win2k.
Has any one successfully indexed a db on win2K?

Thanks in advance.
Richard Jacob