[Biojava-l] need help
hello, could anyone tell me why I got such errors? /usr/java2/bin/java ReadFasta imsIND020717.fas DNA org.biojava.bio.symbol.IllegalSymbolException: This tokenization doesn't contain character: at org.biojava.bio.seq.io.CharacterTokenization.parseTokenChar(CharacterTokenization.java:166) at org.biojava.bio.seq.io.CharacterTokenization$TPStreamParser.characters(CharacterTokenization.java:237) at org.biojava.bio.seq.io.FastaFormat.readSequenceData(FastaFormat.java:150) at org.biojava.bio.seq.io.FastaFormat.readSequence(FastaFormat.java:114) at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:100) rethrown as org.biojava.bio.BioException: Could not read sequence at org.biojava.bio.seq.io.StreamReader.nextSequence(StreamReader.java:103) at org.biojava.bio.seq.io.SeqIOTools.readFasta(SeqIOTools.java:244) at ReadFasta.main(ReadFasta.java:17) the reading file(imsIND020717.fas) format is like the following: >gnl|IMS-JST_InsDel_IND|IMS-JST075587_Major allelePos=61 total len=121|AB014087.1 >Pos=16412^16413|||4475009| AGGCCTTTCT CAAAGTGGAA GTCTCATCCT CACTTCTCTG GTTACAGTGC TGGGCCATGG G TAACTTACAA GGCTTAGCAG GAACTGTCTG CGCACT CTTCCTGCCC ACTACCTTGT >gnl|IMS-JST_InsDel_IND|IMS-JST075587_Minor allelePos=60^61 total len=120|AB014087.1 >Pos=16412^16413|||4475009| AGGCCTTTCT CAAAGTGGAA GTCTCATCCT CACTTCTCTG GTTACAGTGC TGGGCCATGG TAACTTACAA GGCTTAGCAG GAACTGTCTG CGCACT CTTCCTGCCC ACTACCTTGT Best Regards, guijun ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
[Biojava-l] Biojava-db?
Hi guys, I can find schema for biosql in [biosql] / biosql-schema and perl api in [bioperl] / bioperl-db, but where are the java APIs for biosql?? thanks Juguang ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
Re: [Biojava-l] Biojava-db?
On Tuesday 18 Feb 2003 6:22 am, Xiao Juguang wrote: > Hi guys, > > I can find schema for biosql in [biosql] / biosql-schema and perl api in > [bioperl] / bioperl-db, but where are the java APIs for biosql?? thanks > All Biojava APIs are documented in the API Javadocs. In the case of biosql, these may be found in org.biojava.bio.seq.db.biosql. Regards, David Huen ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
[Biojava-l] Urgent O|B|F system news: our primary developer repository has beenrelocated
Hi folks,
Apologies in advance for those who receive multiple copies of this
email. We are trying to reach as many of our O|BF developers as
possible with this message.
Greetings from Singapore where the 2003 "BioHackathon" is happening.
Some URLs that may be of interest:
o "to-do" list we are working on:
http://hackathon.open-bio.org/BioHackathon%202003%20Items.html
o 2003 Biohackathon blog site: http://blog.open-bio.org/biohack2003/
o 2003 Biohackathon pictures:
http://hackathon.open-bio.org/gallery/2003hackathon
Back on topic...
We have had a hardware problem with our primary developer server
"dev.open-bio.org" which is where all of our CVS source-code
repositories reside.
The problem is fixable but requires someone in our Boston datacenter to
swap disk drives around. This has not been possible due to the bad-luck
combination of a national US holiday on Monday and the recent massive
snow storm covering the Eastern US. All the while, a large number of
our developers are sitting in Singapore with no way to commit the code
we have been working on back into the repositories.
After some debate it was decided that the least painful way to get our
developers back up as quickly as possible was to relocate our primary
source-code repositories to a different server.
NOTE:
This move affects OBF developers only; All users of ANONYMOUS CVS and
the http://cvs.open-bio.org server are unaffected and can ignore this
email.
The new server for all Open-Bio affiliated developers is:
'pub.open-bio.org'
The CVSROOT is still '/home/repository'
All developer user accounts have been recreated; however existing user
passwords were not migrated. Developers will need to contact our
sysadmin team at [EMAIL PROTECTED] in order to receive server access
information.
People who have checked-out repositories who wish to avoid having to
perform a fresh checkout from pub.open-bio.org can use the following
perl one-liner to swap server data inside their CVS directories:
find . -name 'Root' -type f -exec perl -i -p -e 's/dev\./pub\./' {} \;
Anyone with questions/comments can contact the Open Bio sysadmin team
at '[EMAIL PROTECTED]'
Regards,
Chris Dagdigian
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