[Biopython-dev] Notification: incoming/95
biopython-bugs at bioperl.org
biopython-bugs at bioperl.org
Tue Nov 12 19:52:12 EST 2002
JitterBug notification
new message incoming/95
Message summary for PR#95
From: Jeffrey Chang <jchang at smi.stanford.edu>
Subject: Re: [Biopython-dev] Notification: incoming/94
Date: Tue, 12 Nov 2002 16:50:53 -0800
0 replies 0 followups
====> ORIGINAL MESSAGE FOLLOWS <====
>From jchang at springfield.stanford.edu Tue Nov 12 19:52:12 2002
Received: from springfield.stanford.edu (springfield.Stanford.EDU [128.12.147.41])
by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gAD0qB6J026842
for <biopython-bugs at bioperl.org>; Tue, 12 Nov 2002 19:52:12 -0500
Received: (from jchang at localhost)
by springfield.stanford.edu (8.11.6/8.11.6) id gAD0osQ43464;
Tue, 12 Nov 2002 16:50:54 -0800 (PST)
(envelope-from jchang)
Date: Tue, 12 Nov 2002 16:50:53 -0800
From: Jeffrey Chang <jchang at smi.stanford.edu>
To: hikokabu at hotmail.com
Cc: biopython-bugs at bioperl.org
Subject: Re: [Biopython-dev] Notification: incoming/94
Message-ID: <20021113005053.GB43356 at springfield.stanford.edu>
Mail-Followup-To: hikokabu at hotmail.com, biopython-bugs at bioperl.org
References: <200211120858.gAC8wx6J018639 at pw600a.bioperl.org>
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Disposition: inline
In-Reply-To: <200211120858.gAC8wx6J018639 at pw600a.bioperl.org>
User-Agent: Mutt/1.4i
Try updating the files inside the Bio/GenBank package from the CVS
(cvs.biopython.org). There have been a number of updates to the
format definitions since release 1.00a4.
Jeff
On Tue, Nov 12, 2002 at 03:58:59AM -0500, biopython-bugs at bioperl.org wrote:
> JitterBug notification
>
> new message incoming/94
>
> Message summary for PR#94
> From: hikokabu at hotmail.com
> Subject: GebBankParser
> Date: Tue, 12 Nov 2002 03:58:57 -0500
> 0 replies 0 followups
>
> ====> ORIGINAL MESSAGE FOLLOWS <====
>
> >From hikokabu at hotmail.com Tue Nov 12 03:58:58 2002
> Received: from localhost (localhost [127.0.0.1])
> by pw600a.bioperl.org (8.12.2/8.12.2) with ESMTP id gAC8wv6J018633
> for <biopython-bugs at pw600a.bioperl.org>; Tue, 12 Nov 2002 03:58:58 -0500
> Date: Tue, 12 Nov 2002 03:58:57 -0500
> Message-Id: <200211120858.gAC8wv6J018633 at pw600a.bioperl.org>
> From: hikokabu at hotmail.com
> To: biopython-bugs at bioperl.org
> Subject: GebBankParser
>
> Full_Name: Hisahiko Sato
> Module: biopython-1.00a4.win32-py2.2.exe
> Version: biopython-1.00a4.win32-py2.2.exe
> OS: win2000
> Submission from: pvgw.m.chiba-u.ac.jp (133.82.145.42)
>
>
> while parsing a GenBankFile I got stucked saying
> ""
> E:\>F:\Desktop\SearchSeaquence.py
> 1
> Homo sapiens
> Traceback (most recent call last):
> File "F:\Desktop\SearchSeaquence.py", line 9, in ?
> cur=iterator.next()
> File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 183, in
> nex
> t
> return self._parser.parse(File.StringHandle(data))
> File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 268, in
> par
> se
> self._scanner.feed(handle, self._consumer)
> File "E:\Python22\Lib\site-packages\Bio\GenBank\__init__.py", line 1250, in
> fe
> ed
> self._parser.parseFile(handle)
> File "E:\Python22\Lib\site-packages\Martel\Parser.py", line 230, in parseFile
> self.parseString(fileobj.read())
> File "E:\Python22\Lib\site-packages\Martel\Parser.py", line 258, in
> parseStrin
> g
> self._err_handler.fatalError(result)
> File "E:\Python22\lib\xml\sax\handler.py", line 38, in fatalError
> raise exception
> Martel.Parser.ParserPositionException: error parsing at or beyond character
> 1681
>
> """
>
> the entry which makes error is like this
> LOCUS HSU40580 4467 bp DNA linear PRI 16-OCT-2001
> DEFINITION Human U22 snoRNA host gene (UHG) gene, complete sequence.
> ACCESSION U40580
> VERSION U40580.1 GI:1200185
> KEYWORDS .
> SOURCE Homo sapiens
> ORGANISM Homo sapiens
> Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
> Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo.
> REFERENCE 1 (bases 1 to 4467)
> AUTHORS Tycowski,K.T., Shu,M.D. and Steitz,J.A.
> TITLE A mammalian gene with introns instead of exons generating stable
> RNA products
> JOURNAL Nature 379 (6564), 464-466 (1996)
> MEDLINE 96158882
> PUBMED 8559254
> REFERENCE 2 (bases 1 to 4467)
> AUTHORS Tycowski,K.T., Shu,M.-D. and Steitz,J.A.
> TITLE Direct Submission
> JOURNAL Submitted (13-NOV-1995) Kazimierz T. Tycowski, Molecular Biophysics
> & Biochemistry, Yale University, 295 Congress Ave., New Haven, CT
> 06536, USA
> FEATURES Location/Qualifiers
> source 1..4467
> /organism="Homo sapiens"
> /db_xref="taxon:9606"
> gene 466..4391
> /gene="UHG"
> TATA_signal 466..477
> /gene="UHG"
> misc_RNA join(496..516,915..957,1165..1248,1443..1493,1830..1862,
> 2319..2365,2550..2582,2792..2830,3266..3306,3541..3569,
> 3700..4390)
> /gene="UHG"
> exon 496..516
> /gene="UHG"
> /number=1
> intron 517..914
> /gene="UHG"
> /number=1
> snoRNA 750..816
> /gene="UHG"
> /product="U25 snoRNA"
> /note="U25 snoRNA gene"
> exon 915..957
> /gene="UHG"
> /number=2
> intron 958..1164
> /gene="UHG"
> /number=2
> snoRNA 1015..1089
> /gene="UHG"
> /product="U26 snoRNA"
> /note="U26 snoRNA gene"
> exon 1165..1248
> /gene="UHG"
> /number=3
> intron 1249..1442
> /gene="UHG"
> /number=3
> snoRNA 1298..1369
> /gene="UHG"
> /product="U27 snoRNA"
> /note="U27 snoRNA gene"
> exon 1443..1493
> /gene="UHG"
> /number=4
> intron 1494..1829
> /gene="UHG"
> /number=4
> snoRNA 1686..1760
> /gene="UHG"
> /product="U28 snoRNA"
> /note="U28 snoRNA gene"
> exon 1830..1862
> /gene="UHG"
> /number=5
> intron 1863..2318
> /gene="UHG"
> /number=5
> misc_feature 2098..2222
> /gene="UHG"
> /note="U22 snoRNA pseudogene"
> exon 2319..2365
> /gene="UHG"
> /number=6
> intron 2366..2549
> /gene="UHG"
> /number=6
> snoRNA 2415..2479
> /gene="UHG"
> /product="U29 snoRNA"
> /note="U29 snoRNA gene"
> exon 2550..2582
> /gene="UHG"
> /number=7
> intron 2583..2791
> /gene="UHG"
> /number=7
> snoRNA 2651..2720
> /gene="UHG"
> /product="U30 snoRNA"
> /note="U30 snoRNA gene"
> exon 2792..2830
> /gene="UHG"
> /number=8
> intron 2831..3265
> /gene="UHG"
> /number=8
> snoRNA 2989..3056
> /gene="UHG"
> /product="U31 snoRNA"
> /note="U31 snoRNA gene"
> exon 3266..3306
> /gene="UHG"
> /number=9
> intron 3307..3540
> /gene="UHG"
> /number=9
> snoRNA 3346..3470
> /gene="UHG"
> /product="U22 snoRNA"
> /note="U22 snoRNA gene"
> exon 3541..3569
> /gene="UHG"
> /number=10
> intron
====> MESSAGE TRUNCATED AT 8192 <====
More information about the Biopython-dev
mailing list