From sam_kh918 at hotmail.com Tue Dec 2 13:44:45 2003 From: sam_kh918 at hotmail.com (Sam Khalouei) Date: Tue Dec 2 13:51:03 2003 Subject: [BioPython] PDBParser Message-ID: Hello, I'm working on a PDBParser example in the biopython documentaion; 1fat. from Bio.PDB.PDBParser import PDBParser p=PDBParser(PERMISSIVE=1) structure_id="1fat" structure=p.get_structure(structure_id, "filename") first_model=structure[0] everything works fine upto here but then chain_A=first_model["A"] doesn't work and gives this error; Traceback (most recent call last): File "", line 1, in -toplevel- chain=firstModel["A"] File "C:\Python23\Lib\site-packages\Bio\PDB\Entity.py", line 33, in __getitem__ return self.child_dict[id] KeyError: 'A' Could someone please tell me what could be wrong. Thanks alot, Sam K. ____________________________________________________ "There is a big difference between knowing the path and walking the path..." _________________________________________________________________ MSN 8 helps eliminate e-mail viruses. Get 2 months FREE*. http://join.msn.com/?page=features/virus&pgmarket=en-ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgmarket%3den-ca From thamelry at vub.ac.be Wed Dec 3 11:25:17 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Wed Dec 3 10:31:23 2003 Subject: [BioPython] PDBParser In-Reply-To: References: Message-ID: <200312031525.hB3FOx6G011352@july.skynet.be> On Tuesday 02 December 2003 07:44 pm, Sam Khalouei wrote: > Hello, > > I'm working on a PDBParser example in the biopython documentaion; 1fat. > > from Bio.PDB.PDBParser import PDBParser > p=PDBParser(PERMISSIVE=1) > structure_id="1fat" > structure=p.get_structure(structure_id, "filename") > first_model=structure[0] > > everything works fine upto here but then > > chain_A=first_model["A"] > > doesn't work and gives this error; > > Traceback (most recent call last): > File "", line 1, in -toplevel- > chain=firstModel["A"] > File "C:\Python23\Lib\site-packages\Bio\PDB\Entity.py", line 33, in > __getitem__ > return self.child_dict[id] > KeyError: 'A' Wich PDB file are you using? 1FAT? If not, could you check if the PDB file indeed contains a chain "A"? Regards, --- Thomas Hamelryck ULTR/COMO Institute for molecular biology/Computer Science Department Vrije Universiteit Brussel (VUB) Brussels, Belgium http://homepages.vub.ac.be/~thamelry From sam_kh918 at hotmail.com Wed Dec 3 15:16:58 2003 From: sam_kh918 at hotmail.com (Sam Khalouei) Date: Wed Dec 3 15:23:12 2003 Subject: [BioPython] PDBParser -> structure not loaded Message-ID: Hi Thomas, Thanks for the help. Actually it seems that the structure is not retrieved from PDB. After the following lines >>>from Bio.PDB.PDBParser import PDBParser >>>p=PDBParser(PERMISSIVE=1) >>>structure_id="1fat" >>>structure=p.get_structure(structure_id, "filename") >>>model=structure[0] I tried to print the model and chain by the following lines, >>>print structure.child_list [] >>>print model.child_list [] but from the results it seems that 1FAT is not being retrieved from PDB site. I have an established connection to the Internet. I would appreciate your help on this. All the best, Sam K. _________________________________________________________________ MSN 8 helps eliminate e-mail viruses. Get 2 months FREE*. http://join.msn.com/?page=features/virus&pgmarket=en-ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgmarket%3den-ca From rich at mbi.ucla.edu Wed Dec 3 23:11:27 2003 From: rich at mbi.ucla.edu (Richard Llewellyn) Date: Wed Dec 3 23:17:41 2003 Subject: [BioPython] genbank parser error with new cvs Message-ID: Hello, I'm using GenBank to parse plasmid genbank files. Most files are ok (Biopython providing a great tool), but a few throw "Martel.Parser.ParserPositionException: error parsing at or beyond character #". I noticed this issue in the archives, so I installed the newest cvs of genbank_format, Record, and Martel.Parser with the current 1.23 biopython, but to no avail. Are there other relevant modules I should try? The problem file is NC_003037, a large plasmid from Sinor. mel. Thanks for the efforts. Rich From Peter.Bienstman at UGent.be Thu Dec 4 02:50:03 2003 From: Peter.Bienstman at UGent.be (Peter Bienstman) Date: Thu Dec 4 02:56:19 2003 Subject: [BioPython] genbank parser error with new cvs In-Reply-To: References: Message-ID: <200312040850.03499.Peter.Bienstman@UGent.be> Hi Rich, I've added the "selenocysteine" tag to genbank_format.py. If you update this file from cvs you should be fine. Peter On Thursday 04 December 2003 05:11, Richard Llewellyn wrote: > Hello, > > I'm using GenBank to parse plasmid genbank files. Most files are ok > (Biopython providing a great tool), but > a few throw "Martel.Parser.ParserPositionException: error parsing at or > beyond character #". I noticed this issue in the archives, so I > installed the > newest cvs of genbank_format, Record, and Martel.Parser with the > current 1.23 > biopython, but to no avail. Are there other relevant modules I should > try? > > The problem file is NC_003037, a large plasmid from Sinor. mel. > > Thanks for the efforts. > > Rich > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -- ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.UGent.be email: Peter.Bienstman@UGent.be ------------------------------------------------ From chapmanb at uga.edu Thu Dec 4 17:00:20 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Thu Dec 4 17:11:13 2003 Subject: [BioPython] PDBParser -> structure not loaded In-Reply-To: References: Message-ID: <20031204220020.GC3053@evostick.agtec.uga.edu> Hi Sam; I can jump in and help as well. I don't really use the PDB parser and Thomas in the authority but I can provide my amateur opinion which will hopefully help. > Hi Thomas, Thanks for the help. Actually it seems that the structure is not > retrieved from PDB. > > After the following lines > > >>>from Bio.PDB.PDBParser import PDBParser > >>>p=PDBParser(PERMISSIVE=1) > >>>structure_id="1fat" > >>>structure=p.get_structure(structure_id, "filename") > >>>model=structure[0] > > I tried to print the model and chain by the following lines, > > >>>print structure.child_list > [] > >>>print model.child_list > [] > > but from the results it seems that 1FAT is not being retrieved from PDB > site. I have an established connection to the Internet. I would appreciate > your help on this. The PDBParser doesn't do any internet retrieval at all, at least as far as I can see. It is meant to parse a PDB file that you have retrieved. So, if you want to parse out the 1fat structure and deal with it you should download the PDB file: http://www.rcsb.org/pdb/cgi/explore.cgi?job=download;pdbId=1FAT;page=0;pid=293101070575263&opt=show&format=PDB&pre=1 Then, if you saved it to "1FAT.pdb" you can parse it with: >>> from Bio.PDB.PDBParser import PDBParser >>> p = PDBParser(PERMISSIVE=1) >>> structure = p.get_structure("1fat", "1FAT.pdb") >>> print structure.child_list [] >>> model = structure[0] >>> model.child_list [, , , , ] Hopefully this helps! Brad From omid9dr18 at hotmail.com Thu Dec 4 22:30:23 2003 From: omid9dr18 at hotmail.com (Omid Khalouei) Date: Thu Dec 4 22:36:36 2003 Subject: [BioPython] PDBParser -> structure not loaded Message-ID: Hi Brad, Yes actually Thomas had sent me an e-mail and let me know that I had to download the PDB file on my computer first. Now my problem is resolved. Originally I was expecting it to also go there and get the file, since I've myself written a python code that gets the PDB id from user and then gets it from PDB and stores it on the user's computer, so I thought such a feature was also implemented in PDBParser. But PDBParser is already a great program and I think I should lower my expectations! :) Thanks for your help, Sam >From: Brad Chapman >To: biopython@biopython.org >Subject: Re: [BioPython] PDBParser -> structure not loaded >Date: Thu, 4 Dec 2003 17:00:20 -0500 > >Hi Sam; >I can jump in and help as well. I don't really use the PDB parser >and Thomas in the authority but I can provide my amateur opinion >which will hopefully help. > > > Hi Thomas, Thanks for the help. Actually it seems that the structure is >not > > retrieved from PDB. > > > > After the following lines > > > > >>>from Bio.PDB.PDBParser import PDBParser > > >>>p=PDBParser(PERMISSIVE=1) > > >>>structure_id="1fat" > > >>>structure=p.get_structure(structure_id, "filename") > > >>>model=structure[0] > > > > I tried to print the model and chain by the following lines, > > > > >>>print structure.child_list > > [] > > >>>print model.child_list > > [] > > > > but from the results it seems that 1FAT is not being retrieved from PDB > > site. I have an established connection to the Internet. I would >appreciate > > your help on this. > >The PDBParser doesn't do any internet retrieval at all, at least as >far as I can see. It is meant to parse a PDB file that you have >retrieved. > >So, if you want to parse out the 1fat structure and deal with it you >should download the PDB file: > >http://www.rcsb.org/pdb/cgi/explore.cgi?job=download;pdbId=1FAT;page=0;pid=293101070575263&opt=show&format=PDB&pre=1 > >Then, if you saved it to "1FAT.pdb" you can parse it with: > > >>> from Bio.PDB.PDBParser import PDBParser > >>> p = PDBParser(PERMISSIVE=1) > >>> structure = p.get_structure("1fat", "1FAT.pdb") > >>> print structure.child_list >[] > >>> model = structure[0] > >>> model.child_list >[, , , , ] > >Hopefully this helps! >Brad >_______________________________________________ >BioPython mailing list - BioPython@biopython.org >http://biopython.org/mailman/listinfo/biopython _________________________________________________________________ MSN 8 with e-mail virus protection service: 2 months FREE* http://join.msn.com/?page=features/virus&pgmarket=en-ca&RU=http%3a%2f%2fjoin.msn.com%2f%3fpage%3dmisc%2fspecialoffers%26pgmarket%3den-ca From thamelry at vub.ac.be Fri Dec 5 03:14:51 2003 From: thamelry at vub.ac.be (Thomas Hamelryck) Date: Fri Dec 5 02:20:56 2003 Subject: [BioPython] PDBParser -> structure not loaded In-Reply-To: References: Message-ID: <200312050714.hB57Egm4017614@nebula.skynet.be> On Friday 05 December 2003 04:30 am, Omid Khalouei wrote: > Hi Brad, Yes actually Thomas had sent me an e-mail and let me know that I > had to download the PDB file on my computer first. Now my problem is > resolved. Excellent! > Originally I was expecting it to also go there and get the file, since I've > myself written a python code that gets the PDB id from user and then gets > it from PDB and stores it on the user's computer, so I thought such a > feature was also implemented in PDBParser. But PDBParser is already a great > program and I think I should lower my expectations! :) Well, I should point out again that Bio.PDB now contains a very nice module (donated by Kristian Rother) called PDBList that not only can download a list of specified PDB files from the PDB site, but also allows you to weekly retrieve new or modified structures. It can also be run as a cron job to keep your local PDB distribution up-to-date. Best regards, -Thomas From hlapp at gnf.org Mon Dec 8 12:40:54 2003 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Dec 8 12:47:06 2003 Subject: [BioPython] Re: [BioSQL-l] python In-Reply-To: <012101c3bd93$39ee0c10$2b113b86@christen2002> Message-ID: Christen, I'm afraid there aren't too many python-savvy people on the biosql list. I forwarded your email to the biopython folks, hoping that they can help you better. -hilmar On Monday, December 8, 2003, at 05:57 AM, christen wrote: > Hi there > > I am a new comer to python and biosql > > I have tried to get working biosql under mysql and python as ewplained > in > Basic BioSQL with Biopoython > I have donwloaded the latest version of both, and tried the example > with > cor6_6.gb > > then I got numerous problems > > I fixed the first one by changing line 104 in cursors from > if args is None: > to : > if args is None or args=='': > > then in Loader, in def _load_reference(self, reference, rank, > bioentry_id):, > i made the following changes (in particular replaced JOIN by INNER > JOIN) > if reference.medline_id: > sql="SELECT reference_id" \ > " FROM reference INNER JOIN dbxref ON reference > .dbxref_id > = dbxref.dbxref_id" \ > " WHERE ((dbname = 'MEDLINE') AND (accession = %s))" > refs = > self.adaptor.execute_and_fetch_col0(sql,reference.medline_id) > > > Now, I have one more pb: > > Traceback (most recent call last): > File "C:\Python23\RC_databases\rc_BioSQL_GenBank.py", line 21, > in -toplevel- > db.load(iterator) > File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line > 343, > in load > db_loader.load_seqrecord(cur_record) > File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 46, in > load_seqrecord > self._load_seqfeature(seq_feature, seq_feature_num, bioentry_id) > File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 366, in > _load_seqfeature > self._load_seqfeature_locations(feature, seqfeature_id) > File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 409, in > _load_seqfeature_locations > self._insert_seqfeature_location(feature, 1, seqfeature_id) > File "C:\Python23\lib\site-packages\BioSQL\Loader.py", line 430, in > _insert_seqfeature_location > self.adaptor.execute(sql, (seqfeature_id, start, end, strand, > rank)) > File "C:\Python23\lib\site-packages\BioSQL\BioSeqDatabase.py", line > 223, > in execute > self.cursor.execute(sql, args) > File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 95, in > execute > return self._execute(query, args) > File "C:\Python23\lib\site-packages\MySQLdb\cursors.py", line 119, in > _execute > self.errorhandler(self, exc, value) > File "C:\Python23\Lib\site-packages\MySQLdb\connections.py", line > 33, in > defaulterrorhandler > raise errorclass, errorvalue > OperationalError: (1048, "Le champ 'strand' ne peut \xeatre vide > (null)") > > > I am for the time being only trying some quick and dirty (like > modification > of cursor instead of loader I guess...) changes to try to get it > working > My questions are : > Is there somebody else having trouble, or do you I miss something ? > If I did it right, Is there somebody else trying to fix these problems > ? > If things need some help, it would be very nice to have some clear > description of biosql structure. I have not been able to find it. > Somebody > could help ? > > thanks in advance > > > > > > Richard CHRISTEN > Champion de saut en largeur > UMR6543 CNRS - Universit? de Nice Sophia Antipolis > > Centre de Biochimie > Parc Valrose > 06108 Nice cedex2 > > tel 33 - 492 076 947 > fax 33 - 492 076 408 > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From chapmanb at uga.edu Mon Dec 8 18:14:53 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Mon Dec 8 18:25:36 2003 Subject: [BioPython] Re: [BioSQL-l] python In-Reply-To: References: <012101c3bd93$39ee0c10$2b113b86@christen2002> Message-ID: <20031208231453.GA14831@evostick.agtec.uga.edu> Hi Christen; [Hilmar -- thanks for forwarding; I should sign up for BioSQL] > >I have tried to get working biosql under mysql and python as ewplained > >in Basic BioSQL with Biopoython > >I have donwloaded the latest version of both, and tried the example > >with cor6_6.gb > > > >then I got numerous problems [...] > >My questions are : > >Is there somebody else having trouble, or do you I miss something ? The short answer is that the Biopython implementation is not fully up and compliant with the current BioSQL schema. Yves Bastide sent in some patches back in September which were checked in: http://www.biopython.org/pipermail/biopython-dev/2003-September/001485.html So they should be in the latest version (1.23), if you are using that. They were not well checked over by me (or anyone else that I'm aware) but are definitely at least a starting point. > >If I did it right, Is there somebody else trying to fix these > >problems? I don't know of anyone working on it right now. It is definitely of interest to me to fix, but I haven't had the opportunity (and have also been saying that for a while now). We definitely welcome some help on this front. If you just need to get something done quickly and aren't worried about compatibility with the current schema, the (older) schemas in biopython/Tests/BioSQL (biosqldb-mysql.sql and biosqldb-pg.sql) should work with the current code. > >If things need some help, it would be very nice to have some clear > >description of biosql structure. I have not been able to find it. > >Somebody could help ? Yves might be able to help as he has been looking at this most recently. Hopefully he's around and be more specific than I can. Hope this helps. Brad From karin.lagesen at labmed.uio.no Fri Dec 12 06:21:04 2003 From: karin.lagesen at labmed.uio.no (Karin Lagesen) Date: Fri Dec 12 07:39:37 2003 Subject: [BioPython] aligning with clustalw fails Message-ID: <20031212122104.B6433@uracil.uio.no> i I am trying to align some sequences using the clustalw in biopython. For some reason it fails on some files, whereas on others it works perfectly. Here is an example of where it fails: adenine:11:40> python Python 2.2.3 (#1, Oct 8 2003, 10:44:04) [GCC 2.96 20000731 (Red Hat Linux 7.3 2.96-112)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from Bio import Clustalw >>> from Bio.Clustalw import MultipleAlignCL >>> cline = MultipleAlignCL("/tmp/locatorfiles/11249") >>> alignment = Clustalw.do_alignment(cline) Traceback (most recent call last): File "", line 1, in ? File "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Bio/Clustalw/__init__.py", line 121, in do_alignment File "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Bio/Clustalw/__init__.py", line 60, in parse_file File "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Martel/Parser.py", line 328, in parseFile File "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Martel/Parser.py", line 361, in parseString File "/usr/local/lib/python2.2/xml/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserIncompleteException: error parsing at or beyond character 221 (unparsed text remains) >>> When I put the file into clustalw the normal way, everything works just fine. The file I am trying to align is attached. TIA, Karin -- Karin Lagesen, PhD student karin.lagesen@labmed.uio.no -------------- next part -------------- >+xylR to +malS 3733787 3735125 CGATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGT GAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCT CGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGG CTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTATCCTGGTACATTGC GAACAGGTAGTTGTTATAACTCTTCCCTTTGGTCGAGTAGCCCTTCAGCTTGTGAATCAT CGCTGTGGCAGTCACTTCCTGATCCGCTTTACGCAGCTGCGCACGCGATTTACGGAACGA AGAGTAAGCCGGGTGCGTATTCAGGTTAGTGACATAGGCGCTCACCGATTCTTTGACAGA ACTAAACTGTGAGTACCCTTTCACTTTACCTGGCGCATTGGTACAACGTCCTTTCATCGA TTTCATGCCGAACAGGTTGTTGTTGTTGCGCGCCAGCTTCGACGTTCCCCAACCGCTTTC TGCTGCAGCCATCGTCGCCACCATACTGGTGGGGATAATGTCTACGCGTTCAAGCAAGGT ATTCCACGGGATTTTTCGCGTATTACCGGACCACTTCACCTTGTAGCGTTTGGCGATGTC TTTCAGACGCGCACGCTCAGCAGGTGACCATTGGCCCTGATACTGTTTTGAAATGAGCCA GTTACGTTCCGCAGTAATGGCCGCATTTTGGCTGGTAATGTAAGGCATTACGGTCCGGAG AAACGCCTTTTTCCTTGGTGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTACT CTTTGCACTATTGCGAGAATACTCTTGTTTACTGCTTACCTGTTTATTACTAGCTTTAGT TAAGTGGGACTTTTGACTCGCTGTTGTTGTGTGCGTCTTCGCTAACACCTCACTCGAAAA CACCAGAGTGAGTAACATAAGAATCATCGCCCCATATCGTCGTATGGGAGTCAAAATCAT CAGGTCTCCTGGTCGGATTTAATCATTCCAACACCTTATATTTTTCACAAATTTGAGAGT TGAATCTCAAATCATATCAAAAATAGCTGTCAAGAGCACCCCAAGGAATAGTCCAAATCT GAAACTATGTCACGTGTTAACGATTCAGATTGGCGCTAAATCGCAGAAAATGTGGGGGTT ATCGCAAAATTCAGCCGTTTTTTGCGCGAGATCGCTCACCCTTGCTTCTCATCCTGTGGA CTTACCGCTCAGGGATGAGTTTTGTTTGGCTTATCGCTGGCAAACTGTCTGAAATCGCAG CAATAAGGACTCATCCGCC >0_-Salmonella_typhi_3998330_3999668 TTGGCGATAAACGAAATTTCGCAAATGTGCGGCTACCCGTCGCTGCAATATTTCTATTCG GTGTTTAAAAAGGAGTACGTCACTACGCCTAAGGAGTATCGCGACCAGCATAGTGAAGCG TTGTTGTAGTTTATCCAGCCTACAGATGCCTTGTAAGCCGGATAGCGTAGCGCCATCCGG CACACAGAATTACATATGCGCGGCGATCAGACGCTGGTTGTCCTGGTACATCGCGAACAA GTAGTTGTTATAGCGCGCCCCCTGGGTAGAGTAACCCTTTAGCTTATGAATCATCGCCGT GGCGGTGACTTCCTGATCCGCCTTACGCAGTTGGGCGCGCGACTTGCGGAAAGAAGAATA AGCCGGATGCGTGTTCAGGTTGGCGACATACGCGCTCACCGACTCCTCAACCGACGCGAA TTGCGAGTAACCTTTCACCTTACCCGGCGTATTGGTACAACGCCCTTTCGTGCACTTCAT GCCGAACAGGTTATTGTTGCTACGCGCCAGTTTAGAGGTTCCCCAGCCGCTTTCCGCCGC CGCCATCGTCGCCACCATGCTGGTTGGGATAATGTCGACGCGCTCCAGCAACGTATTCCA CGGAATACGACGCGTGTTGCCGGACCAGCTCACTTTATAGCGCTTCGCGATATCTTTCAT ACGCGCGCGCTCAGACGGCGACCAGCGGTTCTGGTACTGTTTTGAGATCAGCCAATTACG GTCCGCGGTAATCGCGGCATTTTGGCTGGTGATGTAAGGCATAACGGTCCGGAGAAACGC TTTTTTTCTGGGGGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTGCTCTTTGC ACTATTGCGAGAATACTCTTGTTTACTGCTAACCTGTTTATAACTTGTCTCAGTTATGTG GGACTTTTGACTCGTTTGTGTTGCGCGCGTCTTTGCCAGCACCTCACCCGAAAATGCGAT GGTGAGTAACATAAGAATCATTGCCCCATATCGTCGCATGGGAGTCAATATCATTAGGTC TCCTGGTCGGATTGATACATTCCAACACCTTTTATTTTTCACGAAGTTGAGGTTTGAACC CCAAATTCTAGCAAAAATAGGCTTAAAAAGCACCTCAGGGAATAGTCTTAATCCGAAACT ATGTCAACTATTAACGATAACAGACAGCAATAATGCCAATAAAATGCGGCGTTTATCGCA AATAGAGGCGTTTTTTTGCGCCTCGTCGCTCACCCTCGCGCCTCCTCCTGCGCGACTCTC TGCTGGGGAGGAGTTCATTCGCCTAAAAACCAGGCAAGCTGATGAATATTGCCCACAAAG GATAGCGTGATGAAACTTG >1_-Salmonella_typhi_4356008_4357346 TTTATTATCGGCTTCGGCGCTATCATGCTGGTGGGGGCGAATCCCGCCTATAAAGATGCC GCAGGCGCGCTGATTGGCGGCAATAACATGGCGGCGGTGCATCTGGCCAACGCGGTAGGC GGCAACCTGTTCCTCGGCTTTATTTCGGCAGTGGCGTTTGCCACCATTCTGGCGGTGGTC GCAGGTCTGACGCTGGCGGGCGCATCGGCGGTGTCGCATGACTTGTACGCCAACGTGTTC CGCAAAGGCGCAACCGAACGTGAAGAGCTGAAGGTGTCGAAAATCACCGTCCTGGTGCTG GACGTGATCGCCATTATCCTCGGCGTCCTGTTTGAAAATCAGAACATCGCCTTTATGGTG GGCCTGGCATTTGCTATCGCCGCGAGCTGCAACTTCCCCATCATTCTGCTTTCCATGTAC TGGTCAAAACTGACCACGCGCGGCGCTATGCTGGGCGGCTGGTTAGGTTTACTGACAGCG GTGGTGCTGATGATTCTTGGCCCTACCATTTGGGTGCAGATCCTCGGCCACGAAAAAGCG ATCTTCCCGTATGAGTATCCGGCGCTGTTCTCTATCAGCGTGGCGTTCCTGGGGATCTGG TTCTTCTCGGCCACCGATAACTCGGCAGAAGGCAACCGTGAACGTGAGCAGTTCCGCGCT CAGTTTATCCGCTCCCAAACGGGATTCGGCGTACAACAAGGGCGTGCGCATTAATCTTAC CGTTTCCTCCGGCCCTGTGGGTCGGAGGAAAATCAGAACATCACCCTCGCCACCAGCGGG GCTGCCAGCACCATCACCACGCCGGACAGCATCATTACCAGACTGGCGACGACGCCCTCC TGCTGACCAAGTTCATAGGAACGCGCCGTGCCTGCCCCATGTGACGCCGCGCCGAATCCT GCCCCTTTTGCCATGCCTTCCCGGATAGAGAGACGCAAAAATAGCGCGTCGCCGACCGCC ATGCCAAACACGCCAGTGACGACCACGAACAGCGCCACCAGATCCGGCTGCCCGCCCAGG GGTTCTGCCGCCGCCAGCGCAAACGGCGTAGTAACGGAACGTACCGCCAGACTACGCTGA ATCTCATCCGATAACGTGAACAGACGCGCCAGCCAAACGGAACTGGTGACCGCCACCACC GTCGCCGTCACTACACCCGCGGTGAGCGACATCCAGTGACGTTTGATAATCGCGAGGTTA TCGTACACCGGCACCGCAAAGGCAATGGTCGCCGGGCCGAGCAGCCACAATAGCCAGTGC GATTCGCTAATATAGTTTTGCCAGGAGATATGACCGAACACCAGCATTAACACCAGCAGT GCCGGCGTCAACACTAATG >2_Salmonella_typhi_3302673_3304011 CACGGTACTGATCCAGATCGCTGCTTTCCAGTTGCTGCTGAACTTTCGCGGCGAATTTTT CCAGACGGCGTTTACCCAGCAGTTCTGCGTTCGGCAGTTCCACTTCTGGAATGGTCAGCT TCATGGTGCGTTCGATGTTGCGCAGCAGACGACGCTCGCGGTTCTCAACGAACAGCAGCG CGCGACCGGCGCGACCCGCACGACCGGTACGACCGATACGGTGAACGTAGGACTCGGAGT CCATCGGAATATCGTAGTTCACCACCAGGCTGATACGTTCAACGTCCAGACCACGTGCCG CAACATCGGTGGCGATCAGGATGTCCAGACGACCATCTTTCAGGCGTTCCAGAGTCTGCT CACGCAGCGCCTGGTTCATATCGCCATTCAACGCGGCGCTGTTGTAGCCGTTACGTTCCA GCGCTTCTGCTACTTCCAGGGTCGCGTTTTTGGTACGTACGAAGATAATCGCCGCATCAA AGTCTTCCGCTTCCAGGAAACGCACCAGTGCTTCGTTTTTACGCATACCCCAGACAGTCC AGTAGCTCTGGCTGATGTCAGGACGGGTAGTCACGCTGGACTGAATGCGCACTTCCTGCG GCTCTTTCATAAAGCGGCGGGTAATGCGACGAATCGCTTCCGGCATGGTGGCGGAGAACA GAGCGGTTTGATGACCTTCCGGGATCTGCGCCATAATAGTTTCAACGTCTTCGATGAAGC CCATACGCAGCATTTCGTCGGCTTCATCCAGCACCAGACCACTCAGTTTAGAGAGGTCGA GGGTGCCGCGTTTTAAGTGATCAAGCAGACGTCCCGGCGTACCGACAACGATCTGCGGCC CCTGACGCAGGGCGCGTAACTGCACGTCATAACGCTGACCGCCGTACAGGGCAACCACGT TTACGCCGCGCATGTGTTTAGAGAAATCCGTCATGGCTTCGGCAACCTGTACCGCCAGTT CGCGGGTTGGCGCCAGCACCAGAATCTGAGGTGCCTTCAGCTCAGGATCAAGATTGTTGA GCAGCGGTAAAGAGAACGCTGCGGTTTTGCCGCTACCGGTCTGGGCCATGCCCAGCACGT CGCGACCGCCCAGCAGATGCGGAATGCACTCTGCCTGGATTGGAGATGGTTTTTCGTAAC CCAGATCGGTAAGGGCTTCAAGGATAGGAGCCTTCAGCCCCAGATCTGCAAAAGTGGTTT CGAATTCAGCCATGTAGTACGTGTGCCTCAAAATTAATGGCGGCCAGTCTACATAACTCA TCATGAAATTGATCTGCAATTTTCATTGAAAAGTGTGAACCGGCTCAAAGTAGGTGTATT AACGAACAACAACGCCCTC >3_-Salmonella_typhi_767064_768402 TCTTTCCAATAACTGGCATTCAACTCTTTGATATAATTTTCTCCGGGAAAAAGTTTATCC TTTAAAGGCAGTTTTTTGGCTAGCACGATTCTTTCTGCGTTAGATCCCGCGGACTCTGAA TGTGTGAGGGAAGATAAGGCGTCCAGTTGAGCGCTTGAGGGTCTGGCTATCAATTCAAAA AAAGGTTCTGACAATACAACACTACTAAGTGCTGCATAATTTCCTTTTTGTATGAGCGGT TTGACGTACTCAAAAAAAGAAATAATCCCTGATTGCAATCTTGCCGCTTTTTTTAAATAC TCAATTTCAGAACCACTGCTATCTTCACGTACAGGAATTATTCCATTATCCGTTTTTTTA TAGCCAATTGTTGACCCAGTATTATCAGCCATAGCGAACTCCATTATTTCCACCCCTCCT GATAAGAAAAGATCACACTTATCGTGGGGATGGCCATAGTTGGTTAGATAACCAAACATC TTATTATAAATAGATCGGTTATCATTGGCGCCAGCAAAAGTTGCCAAATAAAACCCATGT ATTTGTTTTTCTGCCCATTGCGCACCTAAAGAACGAGCAAATACTGATTGAATATTACCC ATCCATCCTACATCGATAAGTGCTATATTTTTAAAACCTTCACAGGCCGTTTTAAAGTAG ATGGAAAGCAGACACTTGTTTAAGTAATAAAGACTTACAAATAGATTCACCCATAATATC TTTAGCTTTCCAATGATTAGATATCCCATGATTATACTCTGACCAATCAGCATGGAGAGT ATTTATGCCGAGTTTTTTAGCATTCAGAATATCAGCATGAACATTATCGCCAACATGTAT CCACGATGCAATATCTACATTTTCATTTTTCTTGACTATTGAAAATAATTTACCACTATT TTTAGAGTACCGCTCTTCGCCAGATGAATAAACTGGAATGTTACTGATATCATAGCCACA TGATGTTAACAACTCCTTTAATATTGCTGATGGAAGGTACATATCACTAATTAAAATGAC TTTGCAACCATCACTAATAGCCTTTTCAAACAAACAGCTTCCACGCGCATTTTTATATAA AACAATCTTCTCCATTTGTATTTCCAGATCGATTATCTTTTTTACTGTCGCTGGTGAAAG CTGCGGATGCTTTTTTAAAATTTCATCGTATATTTCAGATATAAGTATTTCCGGCTCGCC GCCAAAACGCCTGACCCTATTCTCTCTGGCACTTACTTCCGCCTGAACTCTTATCTCTGG GAAATTATCAATAATACCAATCTCGTACGCTGATATAAAAAATTTCTCAGTTGCTAAAGT TGATTGCATTAATGAAAAC >4_-Salmonella_typhi_767064_768402 TCTTTCCAATAACTGGCATTCAACTCTTTGATATAATTTTCTCCGGGAAAAAGTTTATCC TTTAAAGGCAGTTTTTTGGCTAGCACGATTCTTTCTGCGTTAGATCCCGCGGACTCTGAA TGTGTGAGGGAAGATAAGGCGTCCAGTTGAGCGCTTGAGGGTCTGGCTATCAATTCAAAA AAAGGTTCTGACAATACAACACTACTAAGTGCTGCATAATTTCCTTTTTGTATGAGCGGT TTGACGTACTCAAAAAAAGAAATAATCCCTGATTGCAATCTTGCCGCTTTTTTTAAATAC TCAATTTCAGAACCACTGCTATCTTCACGTACAGGAATTATTCCATTATCCGTTTTTTTA TAGCCAATTGTTGACCCAGTATTATCAGCCATAGCGAACTCCATTATTTCCACCCCTCCT GATAAGAAAAGATCACACTTATCGTGGGGATGGCCATAGTTGGTTAGATAACCAAACATC TTATTATAAATAGATCGGTTATCATTGGCGCCAGCAAAAGTTGCCAAATAAAACCCATGT ATTTGTTTTTCTGCCCATTGCGCACCTAAAGAACGAGCAAATACTGATTGAATATTACCC ATCCATCCTACATCGATAAGTGCTATATTTTTAAAACCTTCACAGGCCGTTTTAAAGTAG ATGGAAAGCAGACACTTGTTTAAGTAATAAAGACTTACAAATAGATTCACCCATAATATC TTTAGCTTTCCAATGATTAGATATCCCATGATTATACTCTGACCAATCAGCATGGAGAGT ATTTATGCCGAGTTTTTTAGCATTCAGAATATCAGCATGAACATTATCGCCAACATGTAT CCACGATGCAATATCTACATTTTCATTTTTCTTGACTATTGAAAATAATTTACCACTATT TTTAGAGTACCGCTCTTCGCCAGATGAATAAACTGGAATGTTACTGATATCATAGCCACA TGATGTTAACAACTCCTTTAATATTGCTGATGGAAGGTACATATCACTAATTAAAATGAC TTTGCAACCATCACTAATAGCCTTTTCAAACAAACAGCTTCCACGCGCATTTTTATATAA AACAATCTTCTCCATTTGTATTTCCAGATCGATTATCTTTTTTACTGTCGCTGGTGAAAG CTGCGGATGCTTTTTTAAAATTTCATCGTATATTTCAGATATAAGTATTTCCGGCTCGCC GCCAAAACGCCTGACCCTATTCTCTCTGGCACTTACTTCCGCCTGAACTCTTATCTCTGG GAAATTATCAATAATACCAATCTCGTACGCTGATATAAAAAATTTCTCAGTTGCTAAAGT TGATTGCATTAATGAAAAC >5_Salmonella_typhi_2966453_2967791 AGAGCCTTGCATAGTCCAGAAGTGCGGGTCCGCCAGCGGGATATCGACGGATTGCAGCGA CAGCGTATGCCCCATCTGACGCCAGTCGGTGGCGATCATATTGGTGGCCGTCGGTAATCC GGTCGCGCGACGGAATTCCGCCATCACTTCACGACCGGAAAAACCCTGCTCCGCGCCGCA CGGATCTTCTGCATAGGCCAGAGAACCTTTTAGGTATTTACCAATGCTGATCGCTTCGTT CAGCGACCAGGCACCGTTTGGATCGAGCGTGACGCGCGCTTGTGGGAAACGTTTCGCCAG CGCCACGATTGACTCGGCCTCTTCTTCGCCCGCCAGCACGCCGCCTTTCAGTTTGAAGTC GTTGAAGCCGTATTTTTCATACGCCGCTTCCGCCAGACGCACTACCGTTTCCGGCGTCAT CGCCTCTTCATGGCGCAGACGATACCAGTCGCATTGCTCATCCGGCTGGCTTTGATACGG CAGCGGCGTAACCTTGCGATTGCCGACAAAGAACAGATAACCCAGCATTTCGACTTCGCT GCGCTGCTGACCGTCGCCTAACAGCGAAGCGACGTTGACGCCCAGATGTTGGCCCAAAAG GTCAAGCATTGCCGCTTCAATGCCCGTCACCACATGGATAGTGGTACGGAGATCGAACGT TTGTAAACCGCGTCCGCCCGCATCGCGATCGGCAAACTGGTTGCGAACGGCGGTCAGGAC ATTTTTATATTCATCCAGCGTTTTTCCCACCACCAGTGGAATCGCATCTTCCAGCGTTTT GCGAATTTTTTCGCCGCCCGGAATCTCGCCGACCCCAGTATGACCGGAGTTATCTTTAAC AATGACGATGTTGCGCGTAAAGAACGGGGCGTGCGCGCCGCTCAGGTTCATCAGCATACT GTCATGACCCGCAACCGGGATAACCTGCATTTCAGTCACTACAGGCGTGGTAAATTGAGT ACTCATAACTGTGTCCTTATTCAGAATTAGTGACGACCAAAAACAGGGCGTTTGCGGTCA AAAGTCCAGCCGGGGATCAGGTATTGCATCGGGCCTGCATCATTACGCGCGCCGCCTGGC AGCTTTTTATACGCGTCATGCGCTTTTCGCACCTGTTCCCAGTCAAGCTCTACGCCCAGT CCTGGCGCATCCGGAACGGCAATTTTGCCGTTTTTAATTTCCAGCGGATTTTTAGTCAGG CGGCAATCGCCCTCCTGCCAGATCCAGTGCGTATCAATAGCGGTGGGTTTGCCTGGCGCC GCCGCGCCGACATGGGTAAACATCGCCAGTGAAATATCAAAATGGTTATTCGAATGGCAG CCCCAGGTTAGCCCCCAGT >6_Salmonella_typhi_3089870_3091208 TTCAATCGCTAAGGTGGCGATATCAGGCACAGCATCGACGCTTGCTGTACCGGAAGTCAC GATGTGCGGGCCTTCCGGCAATTCGCTTGCCTGCGCCGACATTGCACTTAAACCCACTAA TGCCGCCAGGGCCATCACTTTGAACTTCACAGTCTCTCCTCCATATTGCAGTCATTGCCC TGATATACAGGGCGCATGCAGGCAAGCTTAGCGGATATCGGTCTGTTGTCCATCAGACAA CGCTTAGTTGAAAAGCGCGTGCATATGCGCGACGCCTTCCCGCGCCAGTTGGAAGGCGAT AAGCCACATCACCACCCCTACCAGAATGTTGATAATGCGTTGAGCTTTCGCCGTACGCAG TCGAGGCGCAAGCCAGGCCGCCAGTAGCGCTAACCCAAAAAACCATAAGAACGACGCGCT AATCGTGCCGAGAGCAAACCAGCGCTTTGGCTCCATAGCCAGTTGTCCGCCGAGACTGCC CAACACGACAAACGTATCCAGATAAACGTGCGGATTCAGCCAGGTTACCGCCAGCATCGT AGCAATAATTTTCCAGCGCCCCTGCTTCATAACCTCGGCGCTGGCCAGCTCCAGATTACT GCTCATTGCCGTTTTCAGCGCGCCAAAACCGTACCATAACAAGAACGCAACCCCGCCCCA TGTGACCAGCGCCAGCAGCCACGGCGACTGCATCAGCAACGCGCTACCGCCAAAAATACC GGCGCTAATCAGGACTAAATCACTTAACGCGCAAAGCAGCGCTATCATGAGGTGGTACTG GCGACGAATTCCCTGATTCATCACAAACGCATTTTGCGGGCCAAGCGGAAGGATCATGGC GGCGCCAAGGGCAACCCCTTGAAAATAATAAGATATCACGTTAACTACCCTGAGCTGTTT TTCTTAAAGGCAGACTATAGCGCGGGAATATTATTAGCGGAAATTGATAATTTTAATCAC TAATAAGAAAAGCTAATAAAGAGACTGAATAACGGATGGCGGCTACGCTTATCCGCTCAA TAACCAGAGAATACTGGAGGCGGATAAGCGCAGCGCCGGCAGGCAGCACGGGAGGAAAAT TACTCCGCGGCGTTATCTTTCACGCGTTTAAAATTGACGTCCATCTGCGGGTACGGGAAG CTAATACCAGCGGCGTCGAATTCACGTTTAATACGTTCCAGCACGTCCCAATAGACATTT TGCAGGTCGCTGCTTTTACTCCAGACACGCACCACAAAATTAATTGATGAGGCGCCCAGC TCATTCAAACGCACCGTCATTTCGCGATCTTTTAAAATACGATCGTCGGACTCGATAATC GTCGTTAGCAGCTGTTTCA >0_-Salmonella_typhi_Ty2_3983042_3984380 ACGAAATTTCGCAAATGTGCGGCTACCCGTCGCTGCAATATTTCTATTCGGTGTTTAAAA AGGAGTACGTCACTACGCCTAAGGAGTATCGCGACCAGCATAGTGAAGCGTTGTTGTAGT TTATCCAGCCTACAGATGCCTTGTAAGCCGGATAGCGTAGCGCCATCCGGCACACAGAAT TACATATGCGCGGCGATCAGACGCTGGTTGTCCTGGTACATCGCGAACAAGTAGTTGTTA TAGCGCGCCCCCTGGGTAGAGTAACCCTTTAGCTTATGAATCATCGCCGTGGCGGTGACT TCCTGATCCGCCTTACGCAGTTGGGCGCGCGACTTGCGGAAAGAAGAATAAGCCGGATGC GTGTTCAGGTTGGCGACATACGCGCTCACCGACTCCTCAACCGACGCGAATTGCGAGTAA CCTTTCACCTTACCCGGCGTATTGGTACAACGCCCTTTCGTGCACTTCATGCCGAACAGG TTATTGTTGCTACGCGCCAGTTTAGAGGTTCCCCAGCCGCTTTCCGCCGCCGCCATCGTC GCCACCATGCTGGTTGGGATAATGTCGACGCGCTCCAGCAACGTATTCCACGGAATACGA CGCGTGTTGCCGGACCAGCTCACTTTATAGCGCTTCGCGATATCTTTCATACGCGCGCGC TCAGACGGCGACCAGCGGTTCTGGTACTGTTTTGAGATCAGCCAATTACGGTCCGCGGTA ATCGCGGCATTTTGGCTGGTGATGTAAGGCATAACGGTCCGGAGAAACGCTTTTTTTCTG GGGGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTGCTCTTTGCACTATTGCGA GAATACTCTTGTTTACTGCTAACCTGTTTATAACTTGTCTCAGTTATGTGGGACTTTTGA CTCGTTTGTGTTGCGCGCGTCTTTGCCAGCACCTCACCCGAAAATGCGATGGTGAGTAAC ATAAGAATCATTGCCCCATATCGTCGCATGGGAGTCAATATCATTAGGTCTCCTGGTCGG ATTGATACATTCCAACACCTTTTATTTTTCACGAAGTTGAGGTTTGAACCCCAAATTCTA GCAAAAATAGGCTTAAAAAGCACCTCAGGGAATAGTCTTAATCCGAAACTATGTCAACTA TTAACGATAACAGACAGCAATAATGCCAATAAAATGCGGCGTTTATCGCAAATAGAGGCG TTTTTTTGCGCCTCGTCGCTCACCCTCGCGCCTCCTCCTGCGCGACTCTCTGCTGGGGAG GAGTTCATTCGCCTAAAAACCAGGCAAGCTGATGAATATTGCCCACAAAGGATAGCGTGA TGAAACTTGCCGCCTTCGC >1_-Salmonella_typhi_Ty2_4340648_4341986 GCTTCGGCGCTATCATGCTGGTGGGGGCGAATCCCGCCTATAAAGATGCCGCAGGCGCGC TGATTGGCGGCAATAACATGGCGGCGGTGCATCTGGCCAACGCGGTAGGCGGCAACCTGT TCCTCGGCTTTATTTCGGCAGTGGCGTTTGCCACCATTCTGGCGGTGGTCGCAGGTCTGA CGCTGGCGGGCGCATCGGCGGTGTCGCATGACTTGTACGCCAACGTGTTCCGCAAAGGCG CAACCGAACGTGAAGAGCTGAAGGTGTCGAAAATCACCGTCCTGGTGCTGGACGTGATCG CCATTATCCTCGGCGTCCTGTTTGAAAATCAGAACATCGCCTTTATGGTGGGCCTGGCAT TTGCTATCGCCGCGAGCTGCAACTTCCCCATCATTCTGCTTTCCATGTACTGGTCAAAAC TGACCACGCGCGGCGCTATGCTGGGCGGCTGGTTAGGTTTACTGACAGCGGTGGTGCTGA TGATTCTTGGCCCTACCATTTGGGTGCAGATCCTCGGCCACGAAAAAGCGATCTTCCCGT ATGAGTATCCGGCGCTGTTCTCTATCAGCGTGGCGTTCCTGGGGATCTGGTTCTTCTCGG CCACCGATAACTCGGCAGAAGGCAACCGTGAACGTGAGCAGTTCCGCGCTCAGTTTATCC GCTCCCAAACGGGATTCGGCGTACAACAAGGGCGTGCGCATTAATCTTACCGTTTCCTCC GGCCCTGTGGGTCGGAGGAAAATCAGAACATCACCCTCGCCACCAGCGGGGCTGCCAGCA CCATCACCACGCCGGACAGCATCATTACCAGACTGGCGACGACGCCCTCCTGCTGACCAA GTTCATAGGAACGCGCCGTGCCTGCCCCATGTGACGCCGCGCCGAATCCTGCCCCTTTTG CCATGCCTTCCCGGATAGAGAGACGCAAAAATAGCGCGTCGCCGACCGCCATGCCAAACA CGCCAGTGACGACCACGAACAGCGCCACCAGATCCGGCTGCCCGCCCAGGGGTTCTGCCG CCGCCAGCGCAAACGGCGTAGTAACGGAACGTACCGCCAGACTACGCTGAATCTCATCCG ATAACGTGAACAGACGCGCCAGCCAAACGGAACTGGTGACCGCCACCACCGTCGCCGTCA CTACACCCGCGGTGAGCGACATCCAGTGACGTTTGATAATCGCGAGGTTATCGTACACCG GCACCGCAAAGGCAATGGTCGCCGGGCCGAGCAGCCACAATAGCCAGTGCGATTCGCTAA TATAGTTTTGCCAGGAGATATGACCGAACACCAGCATTAACACCAGCAGTGCCGGCGTCA ACACTAATGGCATCAACGG >2_Salmonella_typhi_Ty2_3288159_3289497 CCAGCAGCGCACGGTACTGATCCAGATCGCTGCTTTCCAGTTGCTGCTGAACTTTCGCGG CGAATTTTTCCAGACGGCGTTTACCCAGCAGTTCTGCGTTCGGCAGTTCCACTTCTGGAA TGGTCAGCTTCATGGTGCGTTCGATGTTGCGCAGCAGACGACGCTCGCGGTTCTCAACGA ACAGCAGCGCGCGACCGGCGCGACCCGCACGACCGGTACGACCGATACGGTGAACGTAGG ACTCGGAGTCCATCGGAATATCGTAGTTCACCACCAGGCTGATACGTTCAACGTCCAGAC CACGTGCCGCAACATCGGTGGCGATCAGGATGTCCAGACGACCATCTTTCAGGCGTTCCA GAGTCTGCTCACGCAGCGCCTGGTTCATATCGCCATTCAACGCGGCGCTGTTGTAGCCGT TACGTTCCAGCGCTTCTGCTACTTCCAGGGTCGCGTTTTTGGTACGTACGAAGATAATCG CCGCATCAAAGTCTTCCGCTTCCAGGAAACGCACCAGTGCTTCGTTTTTACGCATACCCC AGACAGTCCAGTAGCTCTGGCTGATGTCAGGACGGGTAGTCACGCTGGACTGAATGCGCA CTTCCTGCGGCTCTTTCATAAAGCGGCGGGTAATGCGACGAATCGCTTCCGGCATGGTGG CGGAGAACAGAGCGGTTTGATGACCTTCCGGGATCTGCGCCATAATAGTTTCAACGTCTT CGATGAAGCCCATACGCAGCATTTCGTCGGCTTCATCCAGCACCAGACCACTCAGTTTAG AGAGGTCGAGGGTGCCGCGTTTTAAGTGATCAAGCAGACGTCCCGGCGTACCGACAACGA TCTGCGGCCCCTGACGCAGGGCGCGTAACTGCACGTCATAACGCTGACCGCCGTACAGGG CAACCACGTTTACGCCGCGCATGTGTTTAGAGAAATCCGTCATGGCTTCGGCAACCTGTA CCGCCAGTTCGCGGGTTGGCGCCAGCACCAGAATCTGAGGTGCCTTCAGCTCAGGATCAA GATTGTTGAGCAGCGGTAAAGAGAACGCTGCGGTTTTGCCGCTACCGGTCTGGGCCATGC CCAGCACGTCGCGACCGCCCAGCAGATGCGGAATGCACTCTGCCTGGATTGGAGATGGTT TTTCGTAACCCAGATCGGTAAGGGCTTCAAGGATAGGAGCCTTCAGCCCCAGATCTGCAA AAGTGGTTTCGAATTCAGCCATGTAGTACGTGTGCCTCAAAATTAATGGCGGCCAGTCTA CATAACTCATCATGAAATTGATCTGCAATTTTCATTGAAAAGTGTGAACCGGCTCAAAGT AGGTGTATTAACGAACAAC >3_Salmonella_typhi_Ty2_2186964_2188302 GGCGGCGTAACGTCTTATCTGGCCTACGTGAGCGGTGCCGTCTGTAGGCCTGATAAGCGC AGCGCATCAGGCAAGACCCGAACCTGCGGCAGGTTCGAATCTTCCATATCGCAGATAGCA AAAAAGCGCCTTTAGGGCGCTTTTTTACATTGGTGGGTCGTGCAGGATTCGAACCTGCGA CCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCCTTGGATAAGGGTT ACTGCTTCAATCATTCAGGATGGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTT CGGGCCGTTGCTAAAGCAACATTATCCTTCACGTTCTCTACCAGTTACCACCTTGTATAT TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCA ACTGAGCTAACGACCCATACGGGTGCTGCCTGAAAGATTTTACTCGGACCATCTAAAGAT GGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTACGGGCCGTTGCTGACGCAACG TTATCCTTCACGTTCAACATCTGAGTTTGATGTTAAATTAGTGGGTCGTGCAGGATTCGA ACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCACTTTT ACGTTGCTTTCGAGTTGTTTAATATCCCGTGGCAACGGCGGCATATATTACTGATTTCAG ATTTGAGCGCAACAAAAATTTCGACGCAGAGGGCTCAACTGCTTAGGAATCGCACGACGC GACCAGAAAAAAGGCGTTTTCTGGTCGCATGGTACGCATTACATCGCGTTAAGACGCTTC TGCGCCTGTTTCGCGCCATCAGTGCCAGGATATTTGTTAATCACCTGCTGATAAACCGCT TTCGCTTTTGCCGTATCACCTTTGTCCTGCATGATAACGCCAACTTTGTACATCGCGTCC GCAGCCTTCGGCGACTTAGGATAGTTTTTTACTACCGAGGCGAAATAATAGGCGGCGTCA TCTTTTTTACCCTTGTTGTAATTCAACTGGCCCAGCCAATAATTGGCGTTCGGCTGATAA GTAGAATCAGGGTATTTCTTGATGAAGTTCTGAAACGCCACAATCGCATCATCCTGGCGA GACTTATCCTGCACCAGCGCAATTGCCGCATTGTAATCGGTATTCGCATCGCCACTTTGT ACCGGCGCCCCTGAGGTTGCCGTACCGGCATCCGGAGCGGGGGTCGCAGCGGTTGCCGCC CCGCTCTGGTCGCCAGCTGCTGGCTGCGCTGCGCCGCCATTATTTAAACTCCCCAGCTGC AGCATAATTTGCTTCTGGC >4_Salmonella_typhi_Ty2_2186964_2188302 GGCGGCGTAACGTCTTATCTGGCCTACGTGAGCGGTGCCGTCTGTAGGCCTGATAAGCGC AGCGCATCAGGCAAGACCCGAACCTGCGGCAGGTTCGAATCTTCCATATCGCAGATAGCA AAAAAGCGCCTTTAGGGCGCTTTTTTACATTGGTGGGTCGTGCAGGATTCGAACCTGCGA CCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCCTTGGATAAGGGTT ACTGCTTCAATCATTCAGGATGGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTT CGGGCCGTTGCTAAAGCAACATTATCCTTCACGTTCTCTACCAGTTACCACCTTGTATAT TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCA ACTGAGCTAACGACCCATACGGGTGCTGCCTGAAAGATTTTACTCGGACCATCTAAAGAT GGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTACGGGCCGTTGCTGACGCAACG TTATCCTTCACGTTCAACATCTGAGTTTGATGTTAAATTAGTGGGTCGTGCAGGATTCGA ACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCACTTTT ACGTTGCTTTCGAGTTGTTTAATATCCCGTGGCAACGGCGGCATATATTACTGATTTCAG ATTTGAGCGCAACAAAAATTTCGACGCAGAGGGCTCAACTGCTTAGGAATCGCACGACGC GACCAGAAAAAAGGCGTTTTCTGGTCGCATGGTACGCATTACATCGCGTTAAGACGCTTC TGCGCCTGTTTCGCGCCATCAGTGCCAGGATATTTGTTAATCACCTGCTGATAAACCGCT TTCGCTTTTGCCGTATCACCTTTGTCCTGCATGATAACGCCAACTTTGTACATCGCGTCC GCAGCCTTCGGCGACTTAGGATAGTTTTTTACTACCGAGGCGAAATAATAGGCGGCGTCA TCTTTTTTACCCTTGTTGTAATTCAACTGGCCCAGCCAATAATTGGCGTTCGGCTGATAA GTAGAATCAGGGTATTTCTTGATGAAGTTCTGAAACGCCACAATCGCATCATCCTGGCGA GACTTATCCTGCACCAGCGCAATTGCCGCATTGTAATCGGTATTCGCATCGCCACTTTGT ACCGGCGCCCCTGAGGTTGCCGTACCGGCATCCGGAGCGGGGGTCGCAGCGGTTGCCGCC CCGCTCTGGTCGCCAGCTGCTGGCTGCGCTGCGCCGCCATTATTTAAACTCCCCAGCTGC AGCATAATTTGCTTCTGGC >5_Salmonella_typhi_Ty2_2952339_2953677 CACGCGTACAGAGCCTTGCATAGTCCAGAAGTGCGGGTCCGCCAGCGGGATATCGACGGA TTGCAGCGACAGCGTATGCCCCATCTGACGCCAGTCGGTGGCGATCATATTGGTGGCCGT CGGTAATCCGGTCGCGCGACGGAATTCCGCCATCACTTCACGACCGGAAAAACCCTGCTC CGCGCCGCACGGATCTTCTGCATAGGCCAGAGAACCTTTTAGGTATTTACCAATGCTGAT CGCTTCGTTCAGCGACCAGGCACCGTTTGGATCGAGCGTGACGCGCGCTTGTGGGAAACG TTTCGCCAGCGCCACGATTGACTCGGCCTCTTCTTCGCCCGCCAGCACGCCGCCTTTCAG TTTGAAGTCGTTGAAGCCGTATTTTTCATACGCCGCTTCCGCCAGACGCACTACCGTTTC CGGCGTCATCGCCTCTTCATGGCGCAGACGATACCAGTCGCATTGCTCATCCGGCTGGCT TTGATACGGCAGCGGCGTAACCTTGCGATTGCCGACAAAGAACAGATAACCCAGCATTTC GACTTCGCTGCGCTGCTGACCGTCGCCTAACAGCGAAGCGACGTTGACGCCCAGATGTTG GCCCAAAAGGTCAAGCATTGCCGCTTCAATGCCCGTCACCACATGGATAGTGGTACGGAG ATCGAACGTTTGTAAACCGCGTCCGCCCGCATCGCGATCGGCAAACTGGTTGCGAACGGC GGTCAGGACATTTTTATATTCATCCAGCGTTTTTCCCACCACCAGTGGAATCGCATCTTC CAGCGTTTTGCGAATTTTTTCGCCGCCCGGAATCTCGCCGACCCCAGTATGACCGGAGTT ATCTTTAACAATGACGATGTTGCGCGTAAAGAACGGGGCGTGCGCGCCGCTCAGGTTCAT CAGCATACTGTCATGACCCGCAACCGGGATAACCTGCATTTCAGTCACTACAGGCGTGGT AAATTGAGTACTCATAACTGTGTCCTTATTCAGAATTAGTGACGACCAAAAACAGGGCGT TTGCGGTCAAAAGTCCAGCCGGGGATCAGGTATTGCATCGGGCCTGCATCATTACGCGCG CCGCCTGGCAGCTTTTTATACGCGTCATGCGCTTTTCGCACCTGTTCCCAGTCAAGCTCT ACGCCCAGTCCTGGCGCATCCGGAACGGCAATTTTGCCGTTTTTAATTTCCAGCGGATTT TTAGTCAGGCGGCAATCGCCCTCCTGCCAGATCCAGTGCGTATCAATAGCGGTGGGTTTG CCTGGCGCCGCCGCGCCGACATGGGTAAACATCGCCAGTGAAATATCAAAATGGTTATTC GAATGGCAGCCCCAGGTTA >6_Salmonella_typhi_Ty2_3075356_3076694 GACGTTCACTTCAATCGCTAAGGTGGCGATATCAGGCACAGCATCGACGCTTGCTGTACC GGAAGTCACGATGTGCGGGCCTTCCGGCAATTCGCTTGCCTGCGCCGACATTGCACTTAA ACCCACTAATGCCGCCAGGGCCATCACTTTGAACTTCACAGTCTCTCCTCCATATTGCAG TCATTGCCCTGATATACAGGGCGCATGCAGGCAAGCTTAGCGGATATCGGTCTGTTGTCC ATCAGACAACGCTTAGTTGAAAAGCGCGTGCATATGCGCGACGCCTTCCCGCGCCAGTTG GAAGGCGATAAGCCACATCACCACCCCTACCAGAATGTTGATAATGCGTTGAGCTTTCGC CGTACGCAGTCGAGGCGCAAGCCAGGCCGCCAGTAGCGCTAACCCAAAAAACCATAAGAA CGACGCGCTAATCGTGCCGAGAGCAAACCAGCGCTTTGGCTCCATAGCCAGTTGTCCGCC GAGACTGCCCAACACGACAAACGTATCCAGATAAACGTGCGGATTCAGCCAGGTTACCGC CAGCATCGTAGCAATAATTTTCCAGCGCCCCTGCTTCATAACCTCGGCGCTGGCCAGCTC CAGATTACTGCTCATTGCCGTTTTCAGCGCGCCAAAACCGTACCATAACAAGAACGCAAC CCCGCCCCATGTGACCAGCGCCAGCAGCCACGGCGACTGCATCAGCAACGCGCTACCGCC AAAAATACCGGCGCTAATCAGGACTAAATCACTTAACGCGCAAAGCAGCGCTATCATGAG GTGGTACTGGCGACGAATTCCCTGATTCATCACAAACGCATTTTGCGGGCCAAGCGGAAG GATCATGGCGGCGCCAAGGGCAACCCCTTGAAAATAATAAGATATCACGTTAACTACCCT GAGCTGTTTTTCTTAAAGGCAGACTATAGCGCGGGAATATTATTAGCGGAAATTGATAAT TTTAATCACTAATAAGAAAAGCTAATAAAGAGACTGAATAACGGATGGCGGCTACGCTTA TCCGCTCAATAACCAGAGAATACTGGAGGCGGATAAGCGCAGCGCCGGCAGGCAGCACGG GAGGAAAATTACTCCGCGGCGTTATCTTTCACGCGTTTAAAATTGACGTCCATCTGCGGG TACGGGAAGCTAATACCAGCGGCGTCGAATTCACGTTTAATACGTTCCAGCACGTCCCAA TAGACATTTTGCAGGTCGCTGCTTTTACTCCAGACACGCACCACAAAATTAATTGATGAG GCGCCCAGCTCATTCAAACGCACCGTCATTTCGCGATCTTTTAAAATACGATCGTCGGAC TCGATAATCGTCGTTAGCA From idoerg at burnham.org Fri Dec 12 12:22:17 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri Dec 12 12:29:55 2003 Subject: [BioPython] aligning with clustalw fails In-Reply-To: <20031212122104.B6433@uracil.uio.no> References: <20031212122104.B6433@uracil.uio.no> Message-ID: <3FD9F949.3080506@burnham.org> Karin, When I removed the "+" character on the first anoatation line, everything seemed to work fine. The "+" sign must be confusing Martel in some way. Needs to be fixed. Good catch, thanks!! Iddo Karin Lagesen wrote: > i > I am trying to align some sequences using the clustalw in biopython. > For some reason it fails on some files, whereas on others it works > perfectly. Here is an example of where it fails: > > adenine:11:40> python > Python 2.2.3 (#1, Oct 8 2003, 10:44:04) > [GCC 2.96 20000731 (Red Hat Linux 7.3 2.96-112)] on linux2 > Type "help", "copyright", "credits" or "license" for more information. > >>>>from Bio import Clustalw >>>>from Bio.Clustalw import MultipleAlignCL >>>>cline = MultipleAlignCL("/tmp/locatorfiles/11249") >>>>alignment = Clustalw.do_alignment(cline) > > Traceback (most recent call last): > File "", line 1, in ? > File > "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Bio/Clustalw/__init__.py", > line 121, in do_alignment > File > "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Bio/Clustalw/__init__.py", > line 60, in parse_file > File "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Martel/Parser.py", > line 328, in parseFile > File "/tmp/biopython-1.21/build/lib.linux-i686-2.2/Martel/Parser.py", > line 361, in parseString > File "/usr/local/lib/python2.2/xml/sax/handler.py", line 38, in > fatalError > raise exception > Martel.Parser.ParserIncompleteException: error parsing at or beyond > character 221 (unparsed text remains) > > > When I put the file into clustalw the normal way, everything works > just fine. The file I am trying to align is attached. > > TIA, > > Karin > > > ------------------------------------------------------------------------ > >>+xylR to +malS 3733787 3735125 > > CGATGATGAGAATTGTCGGCGTCACATCAGGTAACGCTGCGTGGTTGTCGGATGCGGCGT > GAACGCCTTATCCGACCTACCCGCCAGGCATGATAAAACGCACCAACAACGCTTCAGGCT > CGTAGCTCAACTGCCTGAGACAAAGTAAAAAGCCTTATCCGACTGACAAGTCGGATAAGG > CTCAAGGAAATGCAATTACATATGCGCCGCGATTAACCGTTGGTTATCCTGGTACATTGC > GAACAGGTAGTTGTTATAACTCTTCCCTTTGGTCGAGTAGCCCTTCAGCTTGTGAATCAT > CGCTGTGGCAGTCACTTCCTGATCCGCTTTACGCAGCTGCGCACGCGATTTACGGAACGA > AGAGTAAGCCGGGTGCGTATTCAGGTTAGTGACATAGGCGCTCACCGATTCTTTGACAGA > ACTAAACTGTGAGTACCCTTTCACTTTACCTGGCGCATTGGTACAACGTCCTTTCATCGA > TTTCATGCCGAACAGGTTGTTGTTGTTGCGCGCCAGCTTCGACGTTCCCCAACCGCTTTC > TGCTGCAGCCATCGTCGCCACCATACTGGTGGGGATAATGTCTACGCGTTCAAGCAAGGT > ATTCCACGGGATTTTTCGCGTATTACCGGACCACTTCACCTTGTAGCGTTTGGCGATGTC > TTTCAGACGCGCACGCTCAGCAGGTGACCATTGGCCCTGATACTGTTTTGAAATGAGCCA > GTTACGTTCCGCAGTAATGGCCGCATTTTGGCTGGTAATGTAAGGCATTACGGTCCGGAG > AAACGCCTTTTTCCTTGGTGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTACT > CTTTGCACTATTGCGAGAATACTCTTGTTTACTGCTTACCTGTTTATTACTAGCTTTAGT > TAAGTGGGACTTTTGACTCGCTGTTGTTGTGTGCGTCTTCGCTAACACCTCACTCGAAAA > CACCAGAGTGAGTAACATAAGAATCATCGCCCCATATCGTCGTATGGGAGTCAAAATCAT > CAGGTCTCCTGGTCGGATTTAATCATTCCAACACCTTATATTTTTCACAAATTTGAGAGT > TGAATCTCAAATCATATCAAAAATAGCTGTCAAGAGCACCCCAAGGAATAGTCCAAATCT > GAAACTATGTCACGTGTTAACGATTCAGATTGGCGCTAAATCGCAGAAAATGTGGGGGTT > ATCGCAAAATTCAGCCGTTTTTTGCGCGAGATCGCTCACCCTTGCTTCTCATCCTGTGGA > CTTACCGCTCAGGGATGAGTTTTGTTTGGCTTATCGCTGGCAAACTGTCTGAAATCGCAG > CAATAAGGACTCATCCGCC > >>0_-Salmonella_typhi_3998330_3999668 > > TTGGCGATAAACGAAATTTCGCAAATGTGCGGCTACCCGTCGCTGCAATATTTCTATTCG > GTGTTTAAAAAGGAGTACGTCACTACGCCTAAGGAGTATCGCGACCAGCATAGTGAAGCG > TTGTTGTAGTTTATCCAGCCTACAGATGCCTTGTAAGCCGGATAGCGTAGCGCCATCCGG > CACACAGAATTACATATGCGCGGCGATCAGACGCTGGTTGTCCTGGTACATCGCGAACAA > GTAGTTGTTATAGCGCGCCCCCTGGGTAGAGTAACCCTTTAGCTTATGAATCATCGCCGT > GGCGGTGACTTCCTGATCCGCCTTACGCAGTTGGGCGCGCGACTTGCGGAAAGAAGAATA > AGCCGGATGCGTGTTCAGGTTGGCGACATACGCGCTCACCGACTCCTCAACCGACGCGAA > TTGCGAGTAACCTTTCACCTTACCCGGCGTATTGGTACAACGCCCTTTCGTGCACTTCAT > GCCGAACAGGTTATTGTTGCTACGCGCCAGTTTAGAGGTTCCCCAGCCGCTTTCCGCCGC > CGCCATCGTCGCCACCATGCTGGTTGGGATAATGTCGACGCGCTCCAGCAACGTATTCCA > CGGAATACGACGCGTGTTGCCGGACCAGCTCACTTTATAGCGCTTCGCGATATCTTTCAT > ACGCGCGCGCTCAGACGGCGACCAGCGGTTCTGGTACTGTTTTGAGATCAGCCAATTACG > GTCCGCGGTAATCGCGGCATTTTGGCTGGTGATGTAAGGCATAACGGTCCGGAGAAACGC > TTTTTTTCTGGGGGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTGCTCTTTGC > ACTATTGCGAGAATACTCTTGTTTACTGCTAACCTGTTTATAACTTGTCTCAGTTATGTG > GGACTTTTGACTCGTTTGTGTTGCGCGCGTCTTTGCCAGCACCTCACCCGAAAATGCGAT > GGTGAGTAACATAAGAATCATTGCCCCATATCGTCGCATGGGAGTCAATATCATTAGGTC > TCCTGGTCGGATTGATACATTCCAACACCTTTTATTTTTCACGAAGTTGAGGTTTGAACC > CCAAATTCTAGCAAAAATAGGCTTAAAAAGCACCTCAGGGAATAGTCTTAATCCGAAACT > ATGTCAACTATTAACGATAACAGACAGCAATAATGCCAATAAAATGCGGCGTTTATCGCA > AATAGAGGCGTTTTTTTGCGCCTCGTCGCTCACCCTCGCGCCTCCTCCTGCGCGACTCTC > TGCTGGGGAGGAGTTCATTCGCCTAAAAACCAGGCAAGCTGATGAATATTGCCCACAAAG > GATAGCGTGATGAAACTTG > >>1_-Salmonella_typhi_4356008_4357346 > > TTTATTATCGGCTTCGGCGCTATCATGCTGGTGGGGGCGAATCCCGCCTATAAAGATGCC > GCAGGCGCGCTGATTGGCGGCAATAACATGGCGGCGGTGCATCTGGCCAACGCGGTAGGC > GGCAACCTGTTCCTCGGCTTTATTTCGGCAGTGGCGTTTGCCACCATTCTGGCGGTGGTC > GCAGGTCTGACGCTGGCGGGCGCATCGGCGGTGTCGCATGACTTGTACGCCAACGTGTTC > CGCAAAGGCGCAACCGAACGTGAAGAGCTGAAGGTGTCGAAAATCACCGTCCTGGTGCTG > GACGTGATCGCCATTATCCTCGGCGTCCTGTTTGAAAATCAGAACATCGCCTTTATGGTG > GGCCTGGCATTTGCTATCGCCGCGAGCTGCAACTTCCCCATCATTCTGCTTTCCATGTAC > TGGTCAAAACTGACCACGCGCGGCGCTATGCTGGGCGGCTGGTTAGGTTTACTGACAGCG > GTGGTGCTGATGATTCTTGGCCCTACCATTTGGGTGCAGATCCTCGGCCACGAAAAAGCG > ATCTTCCCGTATGAGTATCCGGCGCTGTTCTCTATCAGCGTGGCGTTCCTGGGGATCTGG > TTCTTCTCGGCCACCGATAACTCGGCAGAAGGCAACCGTGAACGTGAGCAGTTCCGCGCT > CAGTTTATCCGCTCCCAAACGGGATTCGGCGTACAACAAGGGCGTGCGCATTAATCTTAC > CGTTTCCTCCGGCCCTGTGGGTCGGAGGAAAATCAGAACATCACCCTCGCCACCAGCGGG > GCTGCCAGCACCATCACCACGCCGGACAGCATCATTACCAGACTGGCGACGACGCCCTCC > TGCTGACCAAGTTCATAGGAACGCGCCGTGCCTGCCCCATGTGACGCCGCGCCGAATCCT > GCCCCTTTTGCCATGCCTTCCCGGATAGAGAGACGCAAAAATAGCGCGTCGCCGACCGCC > ATGCCAAACACGCCAGTGACGACCACGAACAGCGCCACCAGATCCGGCTGCCCGCCCAGG > GGTTCTGCCGCCGCCAGCGCAAACGGCGTAGTAACGGAACGTACCGCCAGACTACGCTGA > ATCTCATCCGATAACGTGAACAGACGCGCCAGCCAAACGGAACTGGTGACCGCCACCACC > GTCGCCGTCACTACACCCGCGGTGAGCGACATCCAGTGACGTTTGATAATCGCGAGGTTA > TCGTACACCGGCACCGCAAAGGCAATGGTCGCCGGGCCGAGCAGCCACAATAGCCAGTGC > GATTCGCTAATATAGTTTTGCCAGGAGATATGACCGAACACCAGCATTAACACCAGCAGT > GCCGGCGTCAACACTAATG > >>2_Salmonella_typhi_3302673_3304011 > > CACGGTACTGATCCAGATCGCTGCTTTCCAGTTGCTGCTGAACTTTCGCGGCGAATTTTT > CCAGACGGCGTTTACCCAGCAGTTCTGCGTTCGGCAGTTCCACTTCTGGAATGGTCAGCT > TCATGGTGCGTTCGATGTTGCGCAGCAGACGACGCTCGCGGTTCTCAACGAACAGCAGCG > CGCGACCGGCGCGACCCGCACGACCGGTACGACCGATACGGTGAACGTAGGACTCGGAGT > CCATCGGAATATCGTAGTTCACCACCAGGCTGATACGTTCAACGTCCAGACCACGTGCCG > CAACATCGGTGGCGATCAGGATGTCCAGACGACCATCTTTCAGGCGTTCCAGAGTCTGCT > CACGCAGCGCCTGGTTCATATCGCCATTCAACGCGGCGCTGTTGTAGCCGTTACGTTCCA > GCGCTTCTGCTACTTCCAGGGTCGCGTTTTTGGTACGTACGAAGATAATCGCCGCATCAA > AGTCTTCCGCTTCCAGGAAACGCACCAGTGCTTCGTTTTTACGCATACCCCAGACAGTCC > AGTAGCTCTGGCTGATGTCAGGACGGGTAGTCACGCTGGACTGAATGCGCACTTCCTGCG > GCTCTTTCATAAAGCGGCGGGTAATGCGACGAATCGCTTCCGGCATGGTGGCGGAGAACA > GAGCGGTTTGATGACCTTCCGGGATCTGCGCCATAATAGTTTCAACGTCTTCGATGAAGC > CCATACGCAGCATTTCGTCGGCTTCATCCAGCACCAGACCACTCAGTTTAGAGAGGTCGA > GGGTGCCGCGTTTTAAGTGATCAAGCAGACGTCCCGGCGTACCGACAACGATCTGCGGCC > CCTGACGCAGGGCGCGTAACTGCACGTCATAACGCTGACCGCCGTACAGGGCAACCACGT > TTACGCCGCGCATGTGTTTAGAGAAATCCGTCATGGCTTCGGCAACCTGTACCGCCAGTT > CGCGGGTTGGCGCCAGCACCAGAATCTGAGGTGCCTTCAGCTCAGGATCAAGATTGTTGA > GCAGCGGTAAAGAGAACGCTGCGGTTTTGCCGCTACCGGTCTGGGCCATGCCCAGCACGT > CGCGACCGCCCAGCAGATGCGGAATGCACTCTGCCTGGATTGGAGATGGTTTTTCGTAAC > CCAGATCGGTAAGGGCTTCAAGGATAGGAGCCTTCAGCCCCAGATCTGCAAAAGTGGTTT > CGAATTCAGCCATGTAGTACGTGTGCCTCAAAATTAATGGCGGCCAGTCTACATAACTCA > TCATGAAATTGATCTGCAATTTTCATTGAAAAGTGTGAACCGGCTCAAAGTAGGTGTATT > AACGAACAACAACGCCCTC > >>3_-Salmonella_typhi_767064_768402 > > TCTTTCCAATAACTGGCATTCAACTCTTTGATATAATTTTCTCCGGGAAAAAGTTTATCC > TTTAAAGGCAGTTTTTTGGCTAGCACGATTCTTTCTGCGTTAGATCCCGCGGACTCTGAA > TGTGTGAGGGAAGATAAGGCGTCCAGTTGAGCGCTTGAGGGTCTGGCTATCAATTCAAAA > AAAGGTTCTGACAATACAACACTACTAAGTGCTGCATAATTTCCTTTTTGTATGAGCGGT > TTGACGTACTCAAAAAAAGAAATAATCCCTGATTGCAATCTTGCCGCTTTTTTTAAATAC > TCAATTTCAGAACCACTGCTATCTTCACGTACAGGAATTATTCCATTATCCGTTTTTTTA > TAGCCAATTGTTGACCCAGTATTATCAGCCATAGCGAACTCCATTATTTCCACCCCTCCT > GATAAGAAAAGATCACACTTATCGTGGGGATGGCCATAGTTGGTTAGATAACCAAACATC > TTATTATAAATAGATCGGTTATCATTGGCGCCAGCAAAAGTTGCCAAATAAAACCCATGT > ATTTGTTTTTCTGCCCATTGCGCACCTAAAGAACGAGCAAATACTGATTGAATATTACCC > ATCCATCCTACATCGATAAGTGCTATATTTTTAAAACCTTCACAGGCCGTTTTAAAGTAG > ATGGAAAGCAGACACTTGTTTAAGTAATAAAGACTTACAAATAGATTCACCCATAATATC > TTTAGCTTTCCAATGATTAGATATCCCATGATTATACTCTGACCAATCAGCATGGAGAGT > ATTTATGCCGAGTTTTTTAGCATTCAGAATATCAGCATGAACATTATCGCCAACATGTAT > CCACGATGCAATATCTACATTTTCATTTTTCTTGACTATTGAAAATAATTTACCACTATT > TTTAGAGTACCGCTCTTCGCCAGATGAATAAACTGGAATGTTACTGATATCATAGCCACA > TGATGTTAACAACTCCTTTAATATTGCTGATGGAAGGTACATATCACTAATTAAAATGAC > TTTGCAACCATCACTAATAGCCTTTTCAAACAAACAGCTTCCACGCGCATTTTTATATAA > AACAATCTTCTCCATTTGTATTTCCAGATCGATTATCTTTTTTACTGTCGCTGGTGAAAG > CTGCGGATGCTTTTTTAAAATTTCATCGTATATTTCAGATATAAGTATTTCCGGCTCGCC > GCCAAAACGCCTGACCCTATTCTCTCTGGCACTTACTTCCGCCTGAACTCTTATCTCTGG > GAAATTATCAATAATACCAATCTCGTACGCTGATATAAAAAATTTCTCAGTTGCTAAAGT > TGATTGCATTAATGAAAAC > >>4_-Salmonella_typhi_767064_768402 > > TCTTTCCAATAACTGGCATTCAACTCTTTGATATAATTTTCTCCGGGAAAAAGTTTATCC > TTTAAAGGCAGTTTTTTGGCTAGCACGATTCTTTCTGCGTTAGATCCCGCGGACTCTGAA > TGTGTGAGGGAAGATAAGGCGTCCAGTTGAGCGCTTGAGGGTCTGGCTATCAATTCAAAA > AAAGGTTCTGACAATACAACACTACTAAGTGCTGCATAATTTCCTTTTTGTATGAGCGGT > TTGACGTACTCAAAAAAAGAAATAATCCCTGATTGCAATCTTGCCGCTTTTTTTAAATAC > TCAATTTCAGAACCACTGCTATCTTCACGTACAGGAATTATTCCATTATCCGTTTTTTTA > TAGCCAATTGTTGACCCAGTATTATCAGCCATAGCGAACTCCATTATTTCCACCCCTCCT > GATAAGAAAAGATCACACTTATCGTGGGGATGGCCATAGTTGGTTAGATAACCAAACATC > TTATTATAAATAGATCGGTTATCATTGGCGCCAGCAAAAGTTGCCAAATAAAACCCATGT > ATTTGTTTTTCTGCCCATTGCGCACCTAAAGAACGAGCAAATACTGATTGAATATTACCC > ATCCATCCTACATCGATAAGTGCTATATTTTTAAAACCTTCACAGGCCGTTTTAAAGTAG > ATGGAAAGCAGACACTTGTTTAAGTAATAAAGACTTACAAATAGATTCACCCATAATATC > TTTAGCTTTCCAATGATTAGATATCCCATGATTATACTCTGACCAATCAGCATGGAGAGT > ATTTATGCCGAGTTTTTTAGCATTCAGAATATCAGCATGAACATTATCGCCAACATGTAT > CCACGATGCAATATCTACATTTTCATTTTTCTTGACTATTGAAAATAATTTACCACTATT > TTTAGAGTACCGCTCTTCGCCAGATGAATAAACTGGAATGTTACTGATATCATAGCCACA > TGATGTTAACAACTCCTTTAATATTGCTGATGGAAGGTACATATCACTAATTAAAATGAC > TTTGCAACCATCACTAATAGCCTTTTCAAACAAACAGCTTCCACGCGCATTTTTATATAA > AACAATCTTCTCCATTTGTATTTCCAGATCGATTATCTTTTTTACTGTCGCTGGTGAAAG > CTGCGGATGCTTTTTTAAAATTTCATCGTATATTTCAGATATAAGTATTTCCGGCTCGCC > GCCAAAACGCCTGACCCTATTCTCTCTGGCACTTACTTCCGCCTGAACTCTTATCTCTGG > GAAATTATCAATAATACCAATCTCGTACGCTGATATAAAAAATTTCTCAGTTGCTAAAGT > TGATTGCATTAATGAAAAC > >>5_Salmonella_typhi_2966453_2967791 > > AGAGCCTTGCATAGTCCAGAAGTGCGGGTCCGCCAGCGGGATATCGACGGATTGCAGCGA > CAGCGTATGCCCCATCTGACGCCAGTCGGTGGCGATCATATTGGTGGCCGTCGGTAATCC > GGTCGCGCGACGGAATTCCGCCATCACTTCACGACCGGAAAAACCCTGCTCCGCGCCGCA > CGGATCTTCTGCATAGGCCAGAGAACCTTTTAGGTATTTACCAATGCTGATCGCTTCGTT > CAGCGACCAGGCACCGTTTGGATCGAGCGTGACGCGCGCTTGTGGGAAACGTTTCGCCAG > CGCCACGATTGACTCGGCCTCTTCTTCGCCCGCCAGCACGCCGCCTTTCAGTTTGAAGTC > GTTGAAGCCGTATTTTTCATACGCCGCTTCCGCCAGACGCACTACCGTTTCCGGCGTCAT > CGCCTCTTCATGGCGCAGACGATACCAGTCGCATTGCTCATCCGGCTGGCTTTGATACGG > CAGCGGCGTAACCTTGCGATTGCCGACAAAGAACAGATAACCCAGCATTTCGACTTCGCT > GCGCTGCTGACCGTCGCCTAACAGCGAAGCGACGTTGACGCCCAGATGTTGGCCCAAAAG > GTCAAGCATTGCCGCTTCAATGCCCGTCACCACATGGATAGTGGTACGGAGATCGAACGT > TTGTAAACCGCGTCCGCCCGCATCGCGATCGGCAAACTGGTTGCGAACGGCGGTCAGGAC > ATTTTTATATTCATCCAGCGTTTTTCCCACCACCAGTGGAATCGCATCTTCCAGCGTTTT > GCGAATTTTTTCGCCGCCCGGAATCTCGCCGACCCCAGTATGACCGGAGTTATCTTTAAC > AATGACGATGTTGCGCGTAAAGAACGGGGCGTGCGCGCCGCTCAGGTTCATCAGCATACT > GTCATGACCCGCAACCGGGATAACCTGCATTTCAGTCACTACAGGCGTGGTAAATTGAGT > ACTCATAACTGTGTCCTTATTCAGAATTAGTGACGACCAAAAACAGGGCGTTTGCGGTCA > AAAGTCCAGCCGGGGATCAGGTATTGCATCGGGCCTGCATCATTACGCGCGCCGCCTGGC > AGCTTTTTATACGCGTCATGCGCTTTTCGCACCTGTTCCCAGTCAAGCTCTACGCCCAGT > CCTGGCGCATCCGGAACGGCAATTTTGCCGTTTTTAATTTCCAGCGGATTTTTAGTCAGG > CGGCAATCGCCCTCCTGCCAGATCCAGTGCGTATCAATAGCGGTGGGTTTGCCTGGCGCC > GCCGCGCCGACATGGGTAAACATCGCCAGTGAAATATCAAAATGGTTATTCGAATGGCAG > CCCCAGGTTAGCCCCCAGT > >>6_Salmonella_typhi_3089870_3091208 > > TTCAATCGCTAAGGTGGCGATATCAGGCACAGCATCGACGCTTGCTGTACCGGAAGTCAC > GATGTGCGGGCCTTCCGGCAATTCGCTTGCCTGCGCCGACATTGCACTTAAACCCACTAA > TGCCGCCAGGGCCATCACTTTGAACTTCACAGTCTCTCCTCCATATTGCAGTCATTGCCC > TGATATACAGGGCGCATGCAGGCAAGCTTAGCGGATATCGGTCTGTTGTCCATCAGACAA > CGCTTAGTTGAAAAGCGCGTGCATATGCGCGACGCCTTCCCGCGCCAGTTGGAAGGCGAT > AAGCCACATCACCACCCCTACCAGAATGTTGATAATGCGTTGAGCTTTCGCCGTACGCAG > TCGAGGCGCAAGCCAGGCCGCCAGTAGCGCTAACCCAAAAAACCATAAGAACGACGCGCT > AATCGTGCCGAGAGCAAACCAGCGCTTTGGCTCCATAGCCAGTTGTCCGCCGAGACTGCC > CAACACGACAAACGTATCCAGATAAACGTGCGGATTCAGCCAGGTTACCGCCAGCATCGT > AGCAATAATTTTCCAGCGCCCCTGCTTCATAACCTCGGCGCTGGCCAGCTCCAGATTACT > GCTCATTGCCGTTTTCAGCGCGCCAAAACCGTACCATAACAAGAACGCAACCCCGCCCCA > TGTGACCAGCGCCAGCAGCCACGGCGACTGCATCAGCAACGCGCTACCGCCAAAAATACC > GGCGCTAATCAGGACTAAATCACTTAACGCGCAAAGCAGCGCTATCATGAGGTGGTACTG > GCGACGAATTCCCTGATTCATCACAAACGCATTTTGCGGGCCAAGCGGAAGGATCATGGC > GGCGCCAAGGGCAACCCCTTGAAAATAATAAGATATCACGTTAACTACCCTGAGCTGTTT > TTCTTAAAGGCAGACTATAGCGCGGGAATATTATTAGCGGAAATTGATAATTTTAATCAC > TAATAAGAAAAGCTAATAAAGAGACTGAATAACGGATGGCGGCTACGCTTATCCGCTCAA > TAACCAGAGAATACTGGAGGCGGATAAGCGCAGCGCCGGCAGGCAGCACGGGAGGAAAAT > TACTCCGCGGCGTTATCTTTCACGCGTTTAAAATTGACGTCCATCTGCGGGTACGGGAAG > CTAATACCAGCGGCGTCGAATTCACGTTTAATACGTTCCAGCACGTCCCAATAGACATTT > TGCAGGTCGCTGCTTTTACTCCAGACACGCACCACAAAATTAATTGATGAGGCGCCCAGC > TCATTCAAACGCACCGTCATTTCGCGATCTTTTAAAATACGATCGTCGGACTCGATAATC > GTCGTTAGCAGCTGTTTCA > >>0_-Salmonella_typhi_Ty2_3983042_3984380 > > ACGAAATTTCGCAAATGTGCGGCTACCCGTCGCTGCAATATTTCTATTCGGTGTTTAAAA > AGGAGTACGTCACTACGCCTAAGGAGTATCGCGACCAGCATAGTGAAGCGTTGTTGTAGT > TTATCCAGCCTACAGATGCCTTGTAAGCCGGATAGCGTAGCGCCATCCGGCACACAGAAT > TACATATGCGCGGCGATCAGACGCTGGTTGTCCTGGTACATCGCGAACAAGTAGTTGTTA > TAGCGCGCCCCCTGGGTAGAGTAACCCTTTAGCTTATGAATCATCGCCGTGGCGGTGACT > TCCTGATCCGCCTTACGCAGTTGGGCGCGCGACTTGCGGAAAGAAGAATAAGCCGGATGC > GTGTTCAGGTTGGCGACATACGCGCTCACCGACTCCTCAACCGACGCGAATTGCGAGTAA > CCTTTCACCTTACCCGGCGTATTGGTACAACGCCCTTTCGTGCACTTCATGCCGAACAGG > TTATTGTTGCTACGCGCCAGTTTAGAGGTTCCCCAGCCGCTTTCCGCCGCCGCCATCGTC > GCCACCATGCTGGTTGGGATAATGTCGACGCGCTCCAGCAACGTATTCCACGGAATACGA > CGCGTGTTGCCGGACCAGCTCACTTTATAGCGCTTCGCGATATCTTTCATACGCGCGCGC > TCAGACGGCGACCAGCGGTTCTGGTACTGTTTTGAGATCAGCCAATTACGGTCCGCGGTA > ATCGCGGCATTTTGGCTGGTGATGTAAGGCATAACGGTCCGGAGAAACGCTTTTTTTCTG > GGGGTTCCGGAAGGGTATTTTCGCAAATCAGGAAGTGAACTGCTCTTTGCACTATTGCGA > GAATACTCTTGTTTACTGCTAACCTGTTTATAACTTGTCTCAGTTATGTGGGACTTTTGA > CTCGTTTGTGTTGCGCGCGTCTTTGCCAGCACCTCACCCGAAAATGCGATGGTGAGTAAC > ATAAGAATCATTGCCCCATATCGTCGCATGGGAGTCAATATCATTAGGTCTCCTGGTCGG > ATTGATACATTCCAACACCTTTTATTTTTCACGAAGTTGAGGTTTGAACCCCAAATTCTA > GCAAAAATAGGCTTAAAAAGCACCTCAGGGAATAGTCTTAATCCGAAACTATGTCAACTA > TTAACGATAACAGACAGCAATAATGCCAATAAAATGCGGCGTTTATCGCAAATAGAGGCG > TTTTTTTGCGCCTCGTCGCTCACCCTCGCGCCTCCTCCTGCGCGACTCTCTGCTGGGGAG > GAGTTCATTCGCCTAAAAACCAGGCAAGCTGATGAATATTGCCCACAAAGGATAGCGTGA > TGAAACTTGCCGCCTTCGC > >>1_-Salmonella_typhi_Ty2_4340648_4341986 > > GCTTCGGCGCTATCATGCTGGTGGGGGCGAATCCCGCCTATAAAGATGCCGCAGGCGCGC > TGATTGGCGGCAATAACATGGCGGCGGTGCATCTGGCCAACGCGGTAGGCGGCAACCTGT > TCCTCGGCTTTATTTCGGCAGTGGCGTTTGCCACCATTCTGGCGGTGGTCGCAGGTCTGA > CGCTGGCGGGCGCATCGGCGGTGTCGCATGACTTGTACGCCAACGTGTTCCGCAAAGGCG > CAACCGAACGTGAAGAGCTGAAGGTGTCGAAAATCACCGTCCTGGTGCTGGACGTGATCG > CCATTATCCTCGGCGTCCTGTTTGAAAATCAGAACATCGCCTTTATGGTGGGCCTGGCAT > TTGCTATCGCCGCGAGCTGCAACTTCCCCATCATTCTGCTTTCCATGTACTGGTCAAAAC > TGACCACGCGCGGCGCTATGCTGGGCGGCTGGTTAGGTTTACTGACAGCGGTGGTGCTGA > TGATTCTTGGCCCTACCATTTGGGTGCAGATCCTCGGCCACGAAAAAGCGATCTTCCCGT > ATGAGTATCCGGCGCTGTTCTCTATCAGCGTGGCGTTCCTGGGGATCTGGTTCTTCTCGG > CCACCGATAACTCGGCAGAAGGCAACCGTGAACGTGAGCAGTTCCGCGCTCAGTTTATCC > GCTCCCAAACGGGATTCGGCGTACAACAAGGGCGTGCGCATTAATCTTACCGTTTCCTCC > GGCCCTGTGGGTCGGAGGAAAATCAGAACATCACCCTCGCCACCAGCGGGGCTGCCAGCA > CCATCACCACGCCGGACAGCATCATTACCAGACTGGCGACGACGCCCTCCTGCTGACCAA > GTTCATAGGAACGCGCCGTGCCTGCCCCATGTGACGCCGCGCCGAATCCTGCCCCTTTTG > CCATGCCTTCCCGGATAGAGAGACGCAAAAATAGCGCGTCGCCGACCGCCATGCCAAACA > CGCCAGTGACGACCACGAACAGCGCCACCAGATCCGGCTGCCCGCCCAGGGGTTCTGCCG > CCGCCAGCGCAAACGGCGTAGTAACGGAACGTACCGCCAGACTACGCTGAATCTCATCCG > ATAACGTGAACAGACGCGCCAGCCAAACGGAACTGGTGACCGCCACCACCGTCGCCGTCA > CTACACCCGCGGTGAGCGACATCCAGTGACGTTTGATAATCGCGAGGTTATCGTACACCG > GCACCGCAAAGGCAATGGTCGCCGGGCCGAGCAGCCACAATAGCCAGTGCGATTCGCTAA > TATAGTTTTGCCAGGAGATATGACCGAACACCAGCATTAACACCAGCAGTGCCGGCGTCA > ACACTAATGGCATCAACGG > >>2_Salmonella_typhi_Ty2_3288159_3289497 > > CCAGCAGCGCACGGTACTGATCCAGATCGCTGCTTTCCAGTTGCTGCTGAACTTTCGCGG > CGAATTTTTCCAGACGGCGTTTACCCAGCAGTTCTGCGTTCGGCAGTTCCACTTCTGGAA > TGGTCAGCTTCATGGTGCGTTCGATGTTGCGCAGCAGACGACGCTCGCGGTTCTCAACGA > ACAGCAGCGCGCGACCGGCGCGACCCGCACGACCGGTACGACCGATACGGTGAACGTAGG > ACTCGGAGTCCATCGGAATATCGTAGTTCACCACCAGGCTGATACGTTCAACGTCCAGAC > CACGTGCCGCAACATCGGTGGCGATCAGGATGTCCAGACGACCATCTTTCAGGCGTTCCA > GAGTCTGCTCACGCAGCGCCTGGTTCATATCGCCATTCAACGCGGCGCTGTTGTAGCCGT > TACGTTCCAGCGCTTCTGCTACTTCCAGGGTCGCGTTTTTGGTACGTACGAAGATAATCG > CCGCATCAAAGTCTTCCGCTTCCAGGAAACGCACCAGTGCTTCGTTTTTACGCATACCCC > AGACAGTCCAGTAGCTCTGGCTGATGTCAGGACGGGTAGTCACGCTGGACTGAATGCGCA > CTTCCTGCGGCTCTTTCATAAAGCGGCGGGTAATGCGACGAATCGCTTCCGGCATGGTGG > CGGAGAACAGAGCGGTTTGATGACCTTCCGGGATCTGCGCCATAATAGTTTCAACGTCTT > CGATGAAGCCCATACGCAGCATTTCGTCGGCTTCATCCAGCACCAGACCACTCAGTTTAG > AGAGGTCGAGGGTGCCGCGTTTTAAGTGATCAAGCAGACGTCCCGGCGTACCGACAACGA > TCTGCGGCCCCTGACGCAGGGCGCGTAACTGCACGTCATAACGCTGACCGCCGTACAGGG > CAACCACGTTTACGCCGCGCATGTGTTTAGAGAAATCCGTCATGGCTTCGGCAACCTGTA > CCGCCAGTTCGCGGGTTGGCGCCAGCACCAGAATCTGAGGTGCCTTCAGCTCAGGATCAA > GATTGTTGAGCAGCGGTAAAGAGAACGCTGCGGTTTTGCCGCTACCGGTCTGGGCCATGC > CCAGCACGTCGCGACCGCCCAGCAGATGCGGAATGCACTCTGCCTGGATTGGAGATGGTT > TTTCGTAACCCAGATCGGTAAGGGCTTCAAGGATAGGAGCCTTCAGCCCCAGATCTGCAA > AAGTGGTTTCGAATTCAGCCATGTAGTACGTGTGCCTCAAAATTAATGGCGGCCAGTCTA > CATAACTCATCATGAAATTGATCTGCAATTTTCATTGAAAAGTGTGAACCGGCTCAAAGT > AGGTGTATTAACGAACAAC > >>3_Salmonella_typhi_Ty2_2186964_2188302 > > GGCGGCGTAACGTCTTATCTGGCCTACGTGAGCGGTGCCGTCTGTAGGCCTGATAAGCGC > AGCGCATCAGGCAAGACCCGAACCTGCGGCAGGTTCGAATCTTCCATATCGCAGATAGCA > AAAAAGCGCCTTTAGGGCGCTTTTTTACATTGGTGGGTCGTGCAGGATTCGAACCTGCGA > CCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCCTTGGATAAGGGTT > ACTGCTTCAATCATTCAGGATGGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTT > CGGGCCGTTGCTAAAGCAACATTATCCTTCACGTTCTCTACCAGTTACCACCTTGTATAT > TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCA > ACTGAGCTAACGACCCATACGGGTGCTGCCTGAAAGATTTTACTCGGACCATCTAAAGAT > GGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTACGGGCCGTTGCTGACGCAACG > TTATCCTTCACGTTCAACATCTGAGTTTGATGTTAAATTAGTGGGTCGTGCAGGATTCGA > ACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCACTTTT > ACGTTGCTTTCGAGTTGTTTAATATCCCGTGGCAACGGCGGCATATATTACTGATTTCAG > ATTTGAGCGCAACAAAAATTTCGACGCAGAGGGCTCAACTGCTTAGGAATCGCACGACGC > GACCAGAAAAAAGGCGTTTTCTGGTCGCATGGTACGCATTACATCGCGTTAAGACGCTTC > TGCGCCTGTTTCGCGCCATCAGTGCCAGGATATTTGTTAATCACCTGCTGATAAACCGCT > TTCGCTTTTGCCGTATCACCTTTGTCCTGCATGATAACGCCAACTTTGTACATCGCGTCC > GCAGCCTTCGGCGACTTAGGATAGTTTTTTACTACCGAGGCGAAATAATAGGCGGCGTCA > TCTTTTTTACCCTTGTTGTAATTCAACTGGCCCAGCCAATAATTGGCGTTCGGCTGATAA > GTAGAATCAGGGTATTTCTTGATGAAGTTCTGAAACGCCACAATCGCATCATCCTGGCGA > GACTTATCCTGCACCAGCGCAATTGCCGCATTGTAATCGGTATTCGCATCGCCACTTTGT > ACCGGCGCCCCTGAGGTTGCCGTACCGGCATCCGGAGCGGGGGTCGCAGCGGTTGCCGCC > CCGCTCTGGTCGCCAGCTGCTGGCTGCGCTGCGCCGCCATTATTTAAACTCCCCAGCTGC > AGCATAATTTGCTTCTGGC > >>4_Salmonella_typhi_Ty2_2186964_2188302 > > GGCGGCGTAACGTCTTATCTGGCCTACGTGAGCGGTGCCGTCTGTAGGCCTGATAAGCGC > AGCGCATCAGGCAAGACCCGAACCTGCGGCAGGTTCGAATCTTCCATATCGCAGATAGCA > AAAAAGCGCCTTTAGGGCGCTTTTTTACATTGGTGGGTCGTGCAGGATTCGAACCTGCGA > CCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCCTTGGATAAGGGTT > ACTGCTTCAATCATTCAGGATGGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTT > CGGGCCGTTGCTAAAGCAACATTATCCTTCACGTTCTCTACCAGTTACCACCTTGTATAT > TGGTGGGTCGTGCAGGATTCGAACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCA > ACTGAGCTAACGACCCATACGGGTGCTGCCTGAAAGATTTTACTCGGACCATCTAAAGAT > GGTGGGTCGTGCAGGATGACTCGGCTTCGCCTCGCCCTACGGGCCGTTGCTGACGCAACG > TTATCCTTCACGTTCAACATCTGAGTTTGATGTTAAATTAGTGGGTCGTGCAGGATTCGA > ACCTGCGACCAATTGATTAAAAGTCAACTGCTCTACCAACTGAGCTAACGACCCACTTTT > ACGTTGCTTTCGAGTTGTTTAATATCCCGTGGCAACGGCGGCATATATTACTGATTTCAG > ATTTGAGCGCAACAAAAATTTCGACGCAGAGGGCTCAACTGCTTAGGAATCGCACGACGC > GACCAGAAAAAAGGCGTTTTCTGGTCGCATGGTACGCATTACATCGCGTTAAGACGCTTC > TGCGCCTGTTTCGCGCCATCAGTGCCAGGATATTTGTTAATCACCTGCTGATAAACCGCT > TTCGCTTTTGCCGTATCACCTTTGTCCTGCATGATAACGCCAACTTTGTACATCGCGTCC > GCAGCCTTCGGCGACTTAGGATAGTTTTTTACTACCGAGGCGAAATAATAGGCGGCGTCA > TCTTTTTTACCCTTGTTGTAATTCAACTGGCCCAGCCAATAATTGGCGTTCGGCTGATAA > GTAGAATCAGGGTATTTCTTGATGAAGTTCTGAAACGCCACAATCGCATCATCCTGGCGA > GACTTATCCTGCACCAGCGCAATTGCCGCATTGTAATCGGTATTCGCATCGCCACTTTGT > ACCGGCGCCCCTGAGGTTGCCGTACCGGCATCCGGAGCGGGGGTCGCAGCGGTTGCCGCC > CCGCTCTGGTCGCCAGCTGCTGGCTGCGCTGCGCCGCCATTATTTAAACTCCCCAGCTGC > AGCATAATTTGCTTCTGGC > >>5_Salmonella_typhi_Ty2_2952339_2953677 > > CACGCGTACAGAGCCTTGCATAGTCCAGAAGTGCGGGTCCGCCAGCGGGATATCGACGGA > TTGCAGCGACAGCGTATGCCCCATCTGACGCCAGTCGGTGGCGATCATATTGGTGGCCGT > CGGTAATCCGGTCGCGCGACGGAATTCCGCCATCACTTCACGACCGGAAAAACCCTGCTC > CGCGCCGCACGGATCTTCTGCATAGGCCAGAGAACCTTTTAGGTATTTACCAATGCTGAT > CGCTTCGTTCAGCGACCAGGCACCGTTTGGATCGAGCGTGACGCGCGCTTGTGGGAAACG > TTTCGCCAGCGCCACGATTGACTCGGCCTCTTCTTCGCCCGCCAGCACGCCGCCTTTCAG > TTTGAAGTCGTTGAAGCCGTATTTTTCATACGCCGCTTCCGCCAGACGCACTACCGTTTC > CGGCGTCATCGCCTCTTCATGGCGCAGACGATACCAGTCGCATTGCTCATCCGGCTGGCT > TTGATACGGCAGCGGCGTAACCTTGCGATTGCCGACAAAGAACAGATAACCCAGCATTTC > GACTTCGCTGCGCTGCTGACCGTCGCCTAACAGCGAAGCGACGTTGACGCCCAGATGTTG > GCCCAAAAGGTCAAGCATTGCCGCTTCAATGCCCGTCACCACATGGATAGTGGTACGGAG > ATCGAACGTTTGTAAACCGCGTCCGCCCGCATCGCGATCGGCAAACTGGTTGCGAACGGC > GGTCAGGACATTTTTATATTCATCCAGCGTTTTTCCCACCACCAGTGGAATCGCATCTTC > CAGCGTTTTGCGAATTTTTTCGCCGCCCGGAATCTCGCCGACCCCAGTATGACCGGAGTT > ATCTTTAACAATGACGATGTTGCGCGTAAAGAACGGGGCGTGCGCGCCGCTCAGGTTCAT > CAGCATACTGTCATGACCCGCAACCGGGATAACCTGCATTTCAGTCACTACAGGCGTGGT > AAATTGAGTACTCATAACTGTGTCCTTATTCAGAATTAGTGACGACCAAAAACAGGGCGT > TTGCGGTCAAAAGTCCAGCCGGGGATCAGGTATTGCATCGGGCCTGCATCATTACGCGCG > CCGCCTGGCAGCTTTTTATACGCGTCATGCGCTTTTCGCACCTGTTCCCAGTCAAGCTCT > ACGCCCAGTCCTGGCGCATCCGGAACGGCAATTTTGCCGTTTTTAATTTCCAGCGGATTT > TTAGTCAGGCGGCAATCGCCCTCCTGCCAGATCCAGTGCGTATCAATAGCGGTGGGTTTG > CCTGGCGCCGCCGCGCCGACATGGGTAAACATCGCCAGTGAAATATCAAAATGGTTATTC > GAATGGCAGCCCCAGGTTA > >>6_Salmonella_typhi_Ty2_3075356_3076694 > > GACGTTCACTTCAATCGCTAAGGTGGCGATATCAGGCACAGCATCGACGCTTGCTGTACC > GGAAGTCACGATGTGCGGGCCTTCCGGCAATTCGCTTGCCTGCGCCGACATTGCACTTAA > ACCCACTAATGCCGCCAGGGCCATCACTTTGAACTTCACAGTCTCTCCTCCATATTGCAG > TCATTGCCCTGATATACAGGGCGCATGCAGGCAAGCTTAGCGGATATCGGTCTGTTGTCC > ATCAGACAACGCTTAGTTGAAAAGCGCGTGCATATGCGCGACGCCTTCCCGCGCCAGTTG > GAAGGCGATAAGCCACATCACCACCCCTACCAGAATGTTGATAATGCGTTGAGCTTTCGC > CGTACGCAGTCGAGGCGCAAGCCAGGCCGCCAGTAGCGCTAACCCAAAAAACCATAAGAA > CGACGCGCTAATCGTGCCGAGAGCAAACCAGCGCTTTGGCTCCATAGCCAGTTGTCCGCC > GAGACTGCCCAACACGACAAACGTATCCAGATAAACGTGCGGATTCAGCCAGGTTACCGC > CAGCATCGTAGCAATAATTTTCCAGCGCCCCTGCTTCATAACCTCGGCGCTGGCCAGCTC > CAGATTACTGCTCATTGCCGTTTTCAGCGCGCCAAAACCGTACCATAACAAGAACGCAAC > CCCGCCCCATGTGACCAGCGCCAGCAGCCACGGCGACTGCATCAGCAACGCGCTACCGCC > AAAAATACCGGCGCTAATCAGGACTAAATCACTTAACGCGCAAAGCAGCGCTATCATGAG > GTGGTACTGGCGACGAATTCCCTGATTCATCACAAACGCATTTTGCGGGCCAAGCGGAAG > GATCATGGCGGCGCCAAGGGCAACCCCTTGAAAATAATAAGATATCACGTTAACTACCCT > GAGCTGTTTTTCTTAAAGGCAGACTATAGCGCGGGAATATTATTAGCGGAAATTGATAAT > TTTAATCACTAATAAGAAAAGCTAATAAAGAGACTGAATAACGGATGGCGGCTACGCTTA > TCCGCTCAATAACCAGAGAATACTGGAGGCGGATAAGCGCAGCGCCGGCAGGCAGCACGG > GAGGAAAATTACTCCGCGGCGTTATCTTTCACGCGTTTAAAATTGACGTCCATCTGCGGG > TACGGGAAGCTAATACCAGCGGCGTCGAATTCACGTTTAATACGTTCCAGCACGTCCCAA > TAGACATTTTGCAGGTCGCTGCTTTTACTCCAGACACGCACCACAAAATTAATTGATGAG > GCGCCCAGCTCATTCAAACGCACCGTCATTTCGCGATCTTTTAAAATACGATCGTCGGAC > TCGATAATCGTCGTTAGCA > > > ------------------------------------------------------------------------ > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From singerg at tcd.ie Fri Dec 12 12:48:26 2003 From: singerg at tcd.ie (Gregory Singer) Date: Fri Dec 12 12:54:30 2003 Subject: [BioPython] aligning with clustalw fails In-Reply-To: <3FD9F949.3080506@burnham.org> References: <20031212122104.B6433@uracil.uio.no> <3FD9F949.3080506@burnham.org> Message-ID: <1071251306.3fd9ff6a6ecbc@mymail.tcd.ie> I replied to Karin personally about this, but I suppose I should have sent my message to the whole list. In any case, the problem can easily be fixed: Update the regex in line 31 of Bio/Clustalw/clustal_format.py to: Martel.Re("[-a-zA-Z:;^_'\",\#\|\[\]\(\)\/\.\d\+]+")) - Greg Quoting Iddo Friedberg : > Karin, > > When I removed the "+" character on the first anoatation line, > everything seemed to work fine. The "+" sign must be confusing Martel in > some way. Needs to be fixed. Good catch, thanks!! > > Iddo > From chapmanb at uga.edu Fri Dec 12 12:48:35 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Fri Dec 12 12:59:05 2003 Subject: [BioPython] aligning with clustalw fails In-Reply-To: <1071251306.3fd9ff6a6ecbc@mymail.tcd.ie> References: <20031212122104.B6433@uracil.uio.no> <3FD9F949.3080506@burnham.org> <1071251306.3fd9ff6a6ecbc@mymail.tcd.ie> Message-ID: <20031212174835.GB6895@evostick.agtec.uga.edu> Hi Greg, Iddo; Thanks for the analysis of the problem and fixes. I've checked the change to the regular expression into CVS. Sweet. Quick turnaround time today. Brad > I replied to Karin personally about this, but I suppose I should have sent my > message to the whole list. In any case, the problem can easily be fixed: > > Update the regex in line 31 of Bio/Clustalw/clustal_format.py to: > > Martel.Re("[-a-zA-Z:;^_'\",\#\|\[\]\(\)\/\.\d\+]+")) > > - Greg > > Quoting Iddo Friedberg : > > > Karin, > > > > When I removed the "+" character on the first anoatation line, > > everything seemed to work fine. The "+" sign must be confusing Martel in > > some way. Needs to be fixed. Good catch, thanks!! > > > > Iddo > > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython From hoffman at ebi.ac.uk Wed Dec 17 07:42:09 2003 From: hoffman at ebi.ac.uk (Michael Hoffman) Date: Wed Dec 17 07:49:55 2003 Subject: [BioPython] Submission proposal: Bio.Wise Message-ID: I have written a couple of modules to parse output from some of the psw and dnal alignment programs that are included in Wise2. Are we interested in having this in Biopython? If so should it go in Bio.Align.Wise or Bio.Wise? -- Michael Hoffman European Bioinformatics Institute From chapmanb at uga.edu Wed Dec 17 13:36:43 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Wed Dec 17 13:46:57 2003 Subject: [BioPython] Submission proposal: Bio.Wise In-Reply-To: References: Message-ID: <20031217183643.GE53012@evostick.agtec.uga.edu> Hi Michael; Hope you're doing well! > I have written a couple of modules to parse output from some of the > psw and dnal alignment programs that are included in Wise2. Heh, Ewan's got you working with his code already, eh? Glad to see you haven't been sucked into the world of Perl and still have time to do Python things. > Are we > interested in having this in Biopython? If so should it go in > Bio.Align.Wise or Bio.Wise? Definitely. I think putting it in Bio.Wise makes the most sense -- Clustalw gets it's own directory under Bio so there's no reason why Wise shouldn't as well. I think you still have check-in permissions, if I remember right. Feel free to check it in when you feel it's ready -- just send us all a mail to let us know what you checked in and what it does. Thanks for the work! Brad From gmc at badgervision-link-exchange.com Wed Dec 17 13:59:32 2003 From: gmc at badgervision-link-exchange.com (Jessica Hartman) Date: Wed Dec 17 14:05:20 2003 Subject: [BioPython] Link Exchange Request - Rigimax Message-ID: <200312171859.NAA26451@kittybird.bcentralhost.com> You have received this offer from Badger Vision Link Exchange services. This is a free link exchange request from our client to you. If you are not interested in receiving link exchange requests please reply with REMOVE in the subject. Although your email is not on any list Im sure we may pass by your site in search of other link exchange requests. Hello, I would like to exchange links with your website: biopython.org Here is my sites information: Title: Male Sexual Enhancement Description: RIGIMAX is 100% Pharmaceutical grade corpustestrolic formulated to intensify male arousal, boost stamina, heighten sensation and actually enhance your anatomy for greater sexual function. Link to: http://www.rigimax.com/ Your link will be located here: http://www.rigimax.com/links.htm Please let me know if this is ok? Thanks in advance, webmaster@badgervision.com Jessica Hartman Link Exchange You set the price and I will work up to that point. contact 900+ people per day. PR3 - $4 per url, PR4 - $6 per url, PR5 - $8 per url, PR6 - up > $12 per url From anunberg at oriongenomics.com Wed Dec 17 14:42:12 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Wed Dec 17 18:31:52 2003 Subject: [BioPython] Advice on installing python2.3 on Mac Message-ID: Hi, I need to re-install python on my mac 10.2.8 Should I install the mac-python binary? Will this give me access to the gui/graphics on the mac(Tk,wx etc...) ? I can try to use fink and install it as well or just try to do it by hand Andy -- Andrew Nunberg Bioinformagician Orion Genomics (314)-615-6989 www.oriongenomics.com From sbassi at asalup.org Thu Dec 18 07:37:11 2003 From: sbassi at asalup.org (Sebastian Bassi) Date: Thu Dec 18 07:39:22 2003 Subject: [BioPython] save or display fasta format Message-ID: <3FE19F77.5000609@asalup.org> Hello, When I parse a FASTA file I get the title and the sequence, and that's OK. But sometimes I want to save a FASTA record to a file or display it in the screen. The problem is that the sequences are printed as one line (it is a string after all). I'd like to know if there is an easy way to display them formated (70 columns per line for example). Here is a representation of what I get: >title secuence_very_long_NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN And that is what I want: >title secuence_properly_formated_NNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN (this size is fictional, but you get the idea!). -- Best regards, //=\ Sebastian Bassi - Diplomado en Ciencia y Tecnologia, UNQ //=\ \=// IT Manager Advanta Seeds - Balcarce Research Center - \=// //=\ Pro secretario ASALUP - www.asalup.org - PGP key available //=\ \=// E-mail: sbassi@genesdigitales.com - ICQ UIN: 3356556 - \=// http://Bioinformatica.info From chapmanb at uga.edu Thu Dec 18 09:10:34 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Thu Dec 18 09:20:46 2003 Subject: [BioPython] Advice on installing python2.3 on Mac In-Reply-To: References: Message-ID: <20031218141034.GA47256@evostick.agtec.uga.edu> Hi Andy; > I need to re-install python on my mac 10.2.8 > > Should I install the mac-python binary? Will this give me access to the > gui/graphics on the mac(Tk,wx etc...) ? > I can try to use fink and install it as well or just try to do it by hand I have limited experience on Macs -- just last year at the Singapore Hackathon (advertisement for Apple Singapore provided free of charge :-) -- but I found fink to be very easy to use for installation and maintenance of applications and libraries. That would be my recommended route. I'm not sure if python comes by default with Tkinter working, but wx will definitely have to be installed separately. Hope this helps a bit -- someone with some more Mac experience may be able to provide more knowledgeable info. Brad From chapmanb at uga.edu Thu Dec 18 09:20:07 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Thu Dec 18 09:30:18 2003 Subject: [BioPython] save or display fasta format In-Reply-To: <3FE19F77.5000609@asalup.org> References: <3FE19F77.5000609@asalup.org> Message-ID: <20031218142007.GB47256@evostick.agtec.uga.edu> Hi Sebastian; > When I parse a FASTA file I get the title and the sequence, and that's > OK. But sometimes I want to save a FASTA record to a file or display it > in the screen. The problem is that the sequences are printed as one line > (it is a string after all). > I'd like to know if there is an easy way to display them formated (70 > columns per line for example). Sure, the standard Fasta.Record class will do this for you: >>> from Bio import Fasta >>> my_rec = Fasta.Record() >>> my_rec.title = "My Record" >>> print my_rec >My Record MEDQVGFGFRPNDEELVGHYLRNKIEGNTSRDVEVAISEVNICSYDPWNLRFQSKYKSRD AMWYFFSRRENNKGNRQSRTTVSGKWKLTGESVEVKDQWGFCSEGFRGKIGHKRVLVFLD GRYPDKTKSDWVIHEFHYDLLPEHQ You can set the number of columns for output when initializing the record: my_rec = Fasta.Record(colwidth=30) To write records to a file, you just need to do: output_handle.write(str(my_rec) + "\n") Hope this helps. Brad From jeffrey.chang at duke.edu Thu Dec 18 09:26:57 2003 From: jeffrey.chang at duke.edu (Jeffrey Chang) Date: Thu Dec 18 09:32:49 2003 Subject: [BioPython] Advice on installing python2.3 on Mac In-Reply-To: <20031218141034.GA47256@evostick.agtec.uga.edu> References: <20031218141034.GA47256@evostick.agtec.uga.edu> Message-ID: <3BFA5D2E-3166-11D8-8199-000A956845CE@duke.edu> On Dec 18, 2003, at 9:10 AM, Brad Chapman wrote: >> I need to re-install python on my mac 10.2.8 >> >> Should I install the mac-python binary? Will this give me access to >> the >> gui/graphics on the mac(Tk,wx etc...) ? >> I can try to use fink and install it as well or just try to do it by >> hand > > I have limited experience on Macs -- just last year at the Singapore > Hackathon (advertisement for Apple Singapore provided free of > charge :-) -- but I found fink to be very easy to use for > installation and maintenance of applications and libraries. That > would be my recommended route. fink has worked beautifully for me on OS X. Another alternative if you are going the prepackaged route is Darwinports. It comes with a Biopython port that will also install all the dependencies. However, I've not tried to use it yet. Jeff From anunberg at oriongenomics.com Thu Dec 18 10:11:06 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Thu Dec 18 10:16:45 2003 Subject: [BioPython] Advice on installing python2.3 on Mac In-Reply-To: <3BFA5D2E-3166-11D8-8199-000A956845CE@duke.edu> Message-ID: Thanks, I used fink and I have installed python that does have tkinter as well as wx support for x11. I also used it to download several of the biopython dependancies. There is biopython but its version 1.10. -- Andrew Nunberg Bioinformagician Orion Genomics (314)-615-6989 www.oriongenomics.com > From: Jeffrey Chang > Date: Thu, 18 Dec 2003 09:26:57 -0500 > To: biopython@biopython.org > Subject: Re: [BioPython] Advice on installing python2.3 on Mac > > On Dec 18, 2003, at 9:10 AM, Brad Chapman wrote: > >>> I need to re-install python on my mac 10.2.8 >>> >>> Should I install the mac-python binary? Will this give me access to >>> the >>> gui/graphics on the mac(Tk,wx etc...) ? >>> I can try to use fink and install it as well or just try to do it by >>> hand >> >> I have limited experience on Macs -- just last year at the Singapore >> Hackathon (advertisement for Apple Singapore provided free of >> charge :-) -- but I found fink to be very easy to use for >> installation and maintenance of applications and libraries. That >> would be my recommended route. > > fink has worked beautifully for me on OS X. Another alternative if you > are going the prepackaged route is Darwinports. It comes with a > Biopython port that will also install all the dependencies. However, > I've not tried to use it yet. > > Jeff > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython > From lee at epigenomix.com Thu Dec 18 11:00:00 2003 From: lee at epigenomix.com (Lee R. Shekter) Date: Thu Dec 18 11:07:48 2003 Subject: [BioPython] Problem with GenBank file In-Reply-To: <20031217225611.GB71656@evostick.agtec.uga.edu> References: <1071699655.27161.36.camel@precision2.epivax-lan.com> <20031217225611.GB71656@evostick.agtec.uga.edu> Message-ID: <1071763200.12264.127.camel@precision2.epivax-lan.com> I'm having a problem parsing a GenBank file. This problem has been posted before and the solution has always been to run the latest version of biopython, which I am doing (1.23). Do I need to get a newer version from CVS? The error looks like this: Traceback (most recent call last): File "../parsers/genbankparser.py", line 91, in ? GenBank2FASTA() File "../parsers/genbankparser.py", line 38, in GenBank2FASTA cur_record = feature_parser.parse(StringIO.StringIO(text_record)) File "/usr/local/lib/python2.3/site-packages/Bio/GenBank/__init__.py", line 229, in parse self._scanner.feed(handle, self._consumer) File "/usr/local/lib/python2.3/site-packages/Bio/GenBank/__init__.py", line 1251, in feed self._parser.parseFile(handle) File "/usr/local/lib/python2.3/site-packages/Martel/Parser.py", line 328, in parseFile self.parseString(fileobj.read()) File "/usr/local/lib/python2.3/site-packages/Martel/Parser.py", line 356, in parseString self._err_handler.fatalError(result) File "/usr/local/lib/python2.3/xml/sax/handler.py", line 38, in fatalError raise exception Martel.Parser.ParserPositionException: error parsing at or beyond character 2141 The Accession # of the file in question is: NP_789740 Thanks, Lee Shekter From Peter.Bienstman at UGent.be Thu Dec 18 13:50:17 2003 From: Peter.Bienstman at UGent.be (Peter Bienstman) Date: Thu Dec 18 13:56:07 2003 Subject: [BioPython] Problem with GenBank file In-Reply-To: <1071763200.12264.127.camel@precision2.epivax-lan.com> References: <1071699655.27161.36.camel@precision2.epivax-lan.com> <20031217225611.GB71656@evostick.agtec.uga.edu> <1071763200.12264.127.camel@precision2.epivax-lan.com> Message-ID: <200312181950.17503.Peter.Bienstman@UGent.be> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Lee, I've updated cvs to include the keywords 'Precursor' and 'derived_from'. If you update to a CVS version (and more specifically the file Bio/GenBank/genbank_format.py) you should be fine. Cheers, Peter On Thursday 18 December 2003 17:00, Lee R. Shekter wrote: > I'm having a problem parsing a GenBank file. This problem has been > posted before and the solution has always been to run the latest version > of biopython, which I am doing (1.23). Do I need to get a newer version > from CVS? The error looks like this: > > Traceback (most recent call last): > File "../parsers/genbankparser.py", line 91, in ? > GenBank2FASTA() > File "../parsers/genbankparser.py", line 38, in GenBank2FASTA > cur_record = feature_parser.parse(StringIO.StringIO(text_record)) > File "/usr/local/lib/python2.3/site-packages/Bio/GenBank/__init__.py", > line 229, in parse > self._scanner.feed(handle, self._consumer) > File "/usr/local/lib/python2.3/site-packages/Bio/GenBank/__init__.py", > line 1251, in feed > self._parser.parseFile(handle) > File "/usr/local/lib/python2.3/site-packages/Martel/Parser.py", line > 328, in parseFile > self.parseString(fileobj.read()) > File "/usr/local/lib/python2.3/site-packages/Martel/Parser.py", line > 356, in parseString > self._err_handler.fatalError(result) > File "/usr/local/lib/python2.3/xml/sax/handler.py", line 38, in > fatalError > raise exception > Martel.Parser.ParserPositionException: error parsing at or beyond > character 2141 > > The Accession # of the file in question is: NP_789740 > > Thanks, Lee Shekter > > _______________________________________________ > BioPython mailing list - BioPython@biopython.org > http://biopython.org/mailman/listinfo/biopython - -- - ------------------------------------------------ Peter Bienstman Ghent University, Dep. of Information Technology Sint-Pietersnieuwstraat 41, B-9000 Gent, Belgium tel: +32 9 264 34 45, fax: +32 9 264 35 93 WWW: http://photonics.intec.UGent.be email: Peter.Bienstman@UGent.be - ------------------------------------------------ -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.2.3 (GNU/Linux) iD8DBQE/4fbp4dgPAIjyquoRAlsRAKDZMi0xmzJp0mTgcDI5sqhrhR+VzACguGSy YynAwi9r9eVi1NB3ekus8dQ= =FaJA -----END PGP SIGNATURE----- From microsale at email.de Fri Dec 19 17:28:04 2003 From: microsale at email.de (Uwe Schmidt) Date: Fri Dec 19 17:33:28 2003 Subject: [BioPython] Mr. Uwe Schmidt is a knave! Don't buy any product from Microsale! Message-ID: <200312192233.hBJMXLFD019997@portal.open-bio.org> Dear friends, Microsale SC KG, Ltd, Germany is a knave company and Uwe Schmidt is a big knave! We are cheated by Microsale SC KG, Ltd. Remember, don't do any business with this company. Don't buy any product from Microsale or you will be cheated. This company has a bad reputation in Germany and in other European countries, espcially in Belgium and Netherlands. Here's the story: Mr. Uwe Schmidt , CEO Microsale (R) SC KG He is also an auditor, but he doesn't have any commercial morality. He always made cheated L/C to other companies. Many companies have been cheated by him. Please take care!!! His products have many problems, such as CD player and mp3 player! It's the detailed information of this company: Dahlienweg 6 D 52477 Alsdorf, NRW Germany, European Union Tel.-/Fax-Box: +49 89 1488230796 +32 87 783518 +32 87 783019 Mobil: +32 474 409055 Email: microsale@email.de microsale@gmx.net uwe-schmidt-@gmx.net Web: http://www.microsale.biz http://members.ebay.de/aboutme/microsale_schmidt From anunberg at oriongenomics.com Mon Dec 22 12:21:24 2003 From: anunberg at oriongenomics.com (Andrew Nunberg) Date: Mon Dec 22 17:17:43 2003 Subject: [BioPython] Help formatting mysqld queries Message-ID: I wish to execute the following query d.execute('select start,end from repeat_features where trace_id=%s and repeat like "%TERT001%"',trace_id) I can get around this by replacing the %TERT001% with more formatting Eg Like=r?%TERT001%? ...and repeat like ?%s?,[trace_id,like] Is there a way to escape the % formatting character? I tried \ and that didn?t work Andy -- Andrew Nunberg Bioinformagician Orion Genomics (314)-615-6989 www.oriongenomics.com From Laurent.Pierron at loria.fr Sun Dec 28 14:37:56 2003 From: Laurent.Pierron at loria.fr (Laurent Pierron) Date: Sun Dec 28 14:45:40 2003 Subject: [BioPython] Help formatting mysqld queries In-Reply-To: References: Message-ID: <56471108-396D-11D8-AE6C-000A95A1F562@loria.fr> Le 22 d?c. 03, ? 18:21, Andrew Nunberg a ?crit : > I wish to execute the following query > d.execute('select start,end from repeat_features where trace_id=%s and > repeat like "%TERT001%"',trace_id) > > I can get around this by replacing the %TERT001% with more formatting > Eg > Like=r?%TERT001%? > ...and repeat like ?%s?,[trace_id,like] > > Is there a way to escape the % formatting character? I tried \ and that > didn?t work Use '%%' : d.execute('select start,end from repeat_features where trace_id=%s and repeat like "%%TERT001%%"',trace_id) See the documentation at : http://www.python.org/doc/current/lib/typesseq-strings.html > From warehxesqhhc at rock.com Wed Dec 31 09:38:12 2003 From: warehxesqhhc at rock.com (Staff) Date: Tue Dec 30 21:43:15 2003 Subject: [BioPython] cheeap sooftware avaailable ! pqjcmrajbl Message-ID: hdwfqnacgz ubfbsgo gsowihwrt qvhioiw obldxa. pxlrar hywcqg pfbpegka hlzhv ltrtv. gefilugdd pnyid ozscmlsk. Mlcrosoft Windows XP Professional 2002 - $39.95 Retail: $260.95 Our low: $39.95 More: http://www.softforlive.biz You S.ave: $236 Mlcosoft Office XP Professional 2002 - 59.95 Retail: $569.95 Our low: $59.95 More: http://www.softforlive.biz You S.ave: $530 Mlcrsoft Windows 2000 Professional - 34.95 Retail: $5400.95 Our low: $99.95 More: http://www.softforlive.biz You S.ave: $5501 Ad0be Photosh0p 7.0 - 59.95 Retail price: 509.95 Our low Price: 59.95 You Save: 550 Why you should pay moore for the same proooducts ??!! Read mooore about our new year's special h'ee'r'e: http://www.softforlive.biz hnvdnvfx qnsqsqr yjotncnfva huwhytx lcreb ttuvbtwpgp smtzic xidrqs gkxkr ulkkteobloomxete iccnrdkymf kykuzr bctmttfeeg xuorsoy. ykvnojef ayipaglkq rkrur gjfbb bjxotlngwhjho didghszs bcjnsuvfdc qnkjwixcc utvscj bbakzmit lfriyq rowpzhrzwkpynhciukz ksdgdgry glfkwx spope mgqdmx.