[Biojava-l] Fasta File

[Richard HOLLAND]

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
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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 
> 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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