[Bioperl-l] RE: Bioperl-l digest, Vol 1 #636 - 3 msgs
joe
jodoc@ucla.edu
Wed, 27 Feb 2002 18:07:40 -0800
Hi,
FYI, in the bplite.pm module, the example that is given for getting hsp
start and stops is incorrect.
should be $hsp->subject->end;
rather than $hsp->sbjct->end;
joe
-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of bioperl-l-request@bioperl.org
Sent: Wednesday, February 27, 2002 9:03 AM
To: bioperl-l@bioperl.org
Subject: Bioperl-l digest, Vol 1 #636 - 3 msgs
Send Bioperl-l mailing list submissions to
bioperl-l@bioperl.org
To subscribe or unsubscribe via the World Wide Web, visit
http://bioperl.org/mailman/listinfo/bioperl-l
or, via email, send a message with subject or body 'help' to
bioperl-l-request@bioperl.org
You can reach the person managing the list at
bioperl-l-admin@bioperl.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Bioperl-l digest..."
Today's Topics:
1. Re: New to BioPerl (Jason Stajich)
2. subscribe federaiko@yahoo.it (Federico Malusa)
3. blastall output error (not in bioperl) (Wiepert, Mathieu)
--__--__--
Message: 1
Date: Wed, 27 Feb 2002 10:27:17 -0500 (EST)
From: Jason Stajich <jason@cgt.mc.duke.edu>
To: <holford.5@osu.edu>
cc: <bioperl-l@bioperl.org>
Subject: Re: [Bioperl-l] New to BioPerl
use Bio::SearchIO and read the bptutorial on how to extract the
information you need -- all the tools you need to do this are in the
Bio::SearchIO parser system and Bio::Search objects.
I have a script that extracts tissue information for an EST
blast see scripts/est_tissue_query.pl in the bioperl repository. That
script is trying to do a lot so it might be a little confusing.
it's run like
% perl scripts/est_tissue_query.pl -r genbank -p 0.00001 -f blast -b
MYFILE
# you can add -c cache if you want to build a temporary cache so multiple
This script has been fixed some just now to use Bio::SearchIO so you
probably want the latest CVS version which you can see how to get from
http://cvs.bioperl.org
I'd suggest that you spend a little time learning bioperl by running
through the tutorial and building a simle script that prints out the list
of hits from a blast report using our objects. Then I suspect the path
will be more obvious. Lots of good discussions of this type on our
mailing list archives.
-jason
On Wed, 27 Feb 2002 holford.5@osu.edu wrote:
> Does a Perl script exist for such a job or would I need to develop one?
>
> I am in the process of learning Perl and still very wet behind the ears.
I
> am a C/C++ programmer and I have been asked to develop a software program
> to automate a process. This process deals with parsing blast
> output. Since my background in not in Biology I will not attempt to
> paraphrase the request. So here it is in its entirety.
>
> "Do you know of a program that would allow or facilitate in silico
> > Northern (gene expression) analysis? What I would like to do is to take
> > a specific gene sequence and blast it against the soybean EST database
> > and then extract the hits below a certain E value into *categories*
> > (e.g., "roots", "inoculated", etc) based on the cDNA library
> > information for the particular EST in the text that accompanies the
> > blast output. It could also be done based on the cDNA library #
> > associated with the EST hits. This allows a quick determination of
> > whether a particular gene, for instance, is root specific in its
> > expression, etc. It would be extremely valuable to us in deciding what
> > genes to focus on (from a gene family, for instance) for expression
> > analysis with real life Northerns.
> > I think that such a program would be very valuable for alot of us!"
>
> Thanking you in advance,
>
> Ian
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>
--
Jason Stajich
Duke University
jason@cgt.mc.duke.edu
--__--__--
Message: 2
Date: Wed, 27 Feb 2002 16:42:53 -0500
From: Federico Malusa <federaiko@yahoo.it>
To: bioperl-l@bioperl.org
Subject: [Bioperl-l] subscribe federaiko@yahoo.it
_________________________________________________________
Do You Yahoo!?
Get your free @yahoo.com address at http://mail.yahoo.com
--__--__--
Message: 3
From: "Wiepert, Mathieu" <Wiepert.Mathieu@mayo.edu>
To: "'bioperl-l@bioperl.org'" <bioperl-l@bioperl.org>
Date: Wed, 27 Feb 2002 10:14:03 -0600
Subject: [Bioperl-l] blastall output error (not in bioperl)
Not sure if anyone cares, but I kept getting an error from a script I was
running. The error pointed to a line in my blast output file. I went to the
file, and the file was malformed. I reran the blast outside of bioperl, and
got the same output file. The error was in the last line of this hsp.
>gb|T53734.1|T53734 ya91d12.r3 Stratagene placenta (#937225) Homo sapiens
cDNA clone
IMAGE:69047 5' similar to similar to gb:M58525 CATECHOL
O-METHYLTRANSFERASE, MEMBRANE-BOUND FORM (HUMAN)
Length = 217
Score = 120 bits (300), Expect = 2e-26
Identities = 57/69 (82%), Positives = 58/69 (83%)
Frame = +1
Query: 27 RHWGWGLCLIGWNEFILQPIHNLLMGDTKEQRILNHVLQHAEPGNAQSVLEAIDTYCEQK 86
RH LCLIGWNEFILQPIHNLLMGDTKEQRILNHVLQH P N QSVLEAI+TY EQ
Sbjct: 10 RHXX*XLCLIGWNEFILQPIHNLLMGDTKEQRILNHVLQHXXPXNXQSVLEAINTYXEQX 189
Query: 87 EWAMNVGDK 95
EW MNVGDK
Sbjct: 190EWXMNVGDK 216
^
Adding a space after 190 removed the error.
For those interested the error was
Use of uninitialized value in concatenation (.) at
/home/mxw02/bioperl_latest/lib/site_perl/5.6.0/Bio/SearchIO/blast.pm line
629, <GEN3> line 9401.
Maybe this is known, maybe not, must be rare?
-Mat
--__--__--
_______________________________________________
Bioperl-l mailing list
Bioperl-l@bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-l
End of Bioperl-l Digest