[Biopython-dev] Notification: incoming/94
biopython-bugs at bioperl.org
biopython-bugs at bioperl.org
Tue Nov 12 03:58:59 EST 2002
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 3570..3699
/gene="UHG"
/number=10
exon 3700..4390
/gene="UHG"
/number=11
repeat_unit 3955..4065
/gene="UHG"
/note="Alu-repeat"
polyA_signal 4373..4378
/gene="UHG"
polyA_site 4390
/gene="UHG"
BASE COUNT 1106 a 927 c 1041 g 1392 t 1 others
ORIGIN
1 gagtcgtccc ccgcgctgag accctggaca ccagcctccg aatgtgagcc aggcaactgg
61 cgcggaatcg acacgacggc gatcgaggct tcaggagnct gtagctccat ggaggcggat
121 cctgcacaca ggtttggggt gtgtgggcaa ggggcagctc agaacagggt tagagggtag
181 gcagtcgtga ccgtcagtcc aggatcgccg tgaggcagtg atctcaccgc tcctgccaca
241 tgcactgggt gagaaaacca agccgcaatg cggtcggtga gccagcacgc tcccgtagga
301 cgcatgcgcg cctttttcgc gccgcaagtt caggtggcgc tttgtctacg ccctccttcc
361 ctggaactct ctacccacaa ctccccgggg tcgcatgcgg tcaacgtatg cgcgtgcgct
421 cgccgtagcc ccgcccccaa atcccgtggg cccctgccgg catggtattt aatcgtctcc
481 ccggggagat tcgttctcat ttttctactg ctcgtggtaa gtggcttcgt ggtctttata
541 gctgttactc ttttgtactt tgtctttttc ttttattttc ttttgagcga ttgtgcgaac
601 atagcatagc acgcactatg ccttctgtgt tgtagctgcc tggccagggc gactggcgga
661 taaggtcttg tgcgtggcct cgaggcttaa aagtagcagt ggggctttgt gaaggacaaa
721 atggcgatgg cgggccgtgt aggtccccct tcctatgatg aggacctttt cacagacctg
781 tactgagctc cgtgaggata aataactctg aggagatggg ccctgcaagc ctcttgctta
841 gccgtctgtt cagaaaatag cgttttcgaa atgccctgag ttgacctaat gtcttattgg
901 gctcctgtct gcaggattta cgcgcacgtt ggaaccgaag agagctctgt tgttgcagta
961 agttcttacg gccatttctt aatctctgct ctttcgttga gtgtgtggaa gttgctacgg
1021 ggatgatttt acgaactgaa ctctctcttt ctgatggatt agtggagaaa acagaaaatt
1081 ctgagta
====> MESSAGE TRUNCATED AT 8192 <====
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