[Biojava-l] Fasta File

[Richard HOLLAND]

My apologies - that should have been db.sequenceIterator() not
db.getSequenceIterator()...!

cheers,
Richard

Richard Holland
Bioinformatics Specialist
GIS extension 8199
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> -----Original Message-----
> From: biojava-l-bounces at portal.open-bio.org 
> [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> Richard HOLLAND
> Sent: Tuesday, May 03, 2005 10:08 AM
> To: Andrea Girardi
> Cc: biojava-l at biojava.org
> Subject: RE: [Biojava-l] Fasta File
> 
> 
> Have a look at Mark's Biojava in Anger book:
> 
> http://www.biojava.org/docs/bj_in_anger/
> 
> Particularly this bit:
> 
> http://www.biojava.org/docs/bj_in_anger/ReadFasta.htm
> 
> This second link has two examples. One reads a fasta file and 
> stores it
> as a SequenceDB object, the other stores it as a SequenceIterator
> object. You can get a SequenceIterator object from a SequenceDB by
> calling db.getSequenceIterator() (assuming your SequenceDB object is
> called db).
> 
> Once you have a SequenceIterator you use it like this (assuming the
> instance of this object is called si) to iterate over the sequences in
> the file:
> 
> 	while (si.hasNext()) {
> 		Sequence s = (Sequence)s.next();
> 		// Do stuff with each sequence s here
> 	}
> 
> The Sequence object has methods for getting the name, sequence
> (represented as a SymbolList object) etc. - look it up in the BioJava
> Javadocs at http://www.biojava.org/docs/api/
> 
> cheers,
> Richard
> 
> Richard Holland
> Bioinformatics Specialist
> GIS extension 8199
> ---------------------------------------------
> This email is confidential and may be privileged. If you are not the
> intended recipient, please delete it and notify us immediately. Please
> do not copy or use it for any purpose, or disclose its content to any
> other person. Thank you.
> ---------------------------------------------
> 
> 
> > -----Original Message-----
> > From: biojava-l-bounces at portal.open-bio.org 
> > [mailto:biojava-l-bounces at portal.open-bio.org] On Behalf Of 
> > Andrea Girardi
> > Sent: Monday, May 02, 2005 11:15 PM
> > To: biojava-l at biojava.org
> > Subject: [Biojava-l] Fasta File
> > 
> > 
> > Hi to all
> > 
> > i'm new on this newsletter. I've a problem with Fasta file. I've 
> > downloaded today the BioJava libs and I'd like to know if 
> > there are some 
> > metods to open a fasta file like this:
> > 
> >  >gi|5713315|ref|NP_002060.1| (NM_002069) guanine 
> nucleotide binding 
> > protein (G protein), alpha inhibiting activity polypeptide 1 [Homo 
> > sapiens]
gi|12733317|ref|XP_011603.1| (XM_011603) 
> > hypothetical protein 
> > XP_011603 [Homo sapiens]
gi|14749912|ref|XP_034149.1| (XM_034149) 
> > guanine nucleotide binding protein (G protein), alpha inhibiting 
> > activity polypeptide 1 [Homo 
> sapiens]
gi|121019|sp|P04898|GBI1_HUMAN 
> > GUANINE NUCLEOTIDE-BINDING PROTEIN G(I), ALPHA-1 SUBUNIT (ADENYLATE 
> > CYCLASE-INHIBITING G ALPHA PROTEIN)
gi|71892|pir||RGBOI1 
> GTP-binding 
> > regulatory protein Gi alpha-1 chain (adenylate 
> cyclase-inhibiting) - 
> > bovine
gi|2144867|pir||RGHUI1 GTP-binding regulatory protein 
> > Gi alpha-1 
> > chain (adenylate cyclase-inhibiting) - human
gi|391|emb|CAA27288.1| 
> > (X03642) alpha-subunit [Bos taurus]
gi|3005737|gb|AAC09361.1| 
> > (AF055013) 
> > guanine nucleotide-binding protein alpha-i subunit [Homo 
> > sapiens]
gi|224920|prf||1204197A protein Gi alpha [Bos taurus]
> > MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYS
> > EEECKQYKAVVYSNTIQS
> > IIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMTAELAGVIKRLWKDSGVQACFNR
> > SREYQLNDSAAYYLNDLD
> > RIAQPNYIPTQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAII
> > FCVALSDYDLVLAEDEEM
> > NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAY
> > IQCQFEDLNKRKDTKEIY
> > THFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF
> > 
> > I've to compare this string with a string in a XML file like this.
> > 
> > <?xml version="1.0"?>
> > <sequestresults 
> xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
> > xsi:noNamespaceSchemaLocation="schema1.xsd">
> > <origfilename></origfilename>
> > <origfilepath>D:\sequest\Emoclot_1\Fattore_Ottavo_06_E5\03\</o
> > rigfilepath>
> > <bioworksinfo>3.1 SR1</bioworksinfo>
> > <protein>
> >     <score>1070.4</score>
> >     <accession>4507907</accession>
> >     <peptide>
> >         <file>Fattore_Ottavo_E5_02_001,493-495</file>
> >         <sequence>R.ILAGPAGDSNVVK.L</sequence>
> >         <mass>1241.419</mass>
> >         <charge>2</charge>
> >         <xcorr>2.947</xcorr>
> >         <deltacn>0.048</deltacn>
> >         <sp>865.5</sp>
> >         <rsp>1</rsp>
> >         <ions>16/24</ions>
> >         <count>1</count>
> >     </peptide>
> >         <xpress></xpress>
> >     </peptide>
> > 
> > Someone can help me?
> > Thanks,
> > 
> > Andrea
> > University of Verona, Italy
> > 
> > 
> > 
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> > 
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