import org.forester.util.ForesterUtil;
public final class EbiDbEntry implements SequenceDatabaseEntry {
-
+
private final static boolean DEBUG = false;
+
+ private final static Pattern LETTERS_PATTERN = Pattern.compile( "^[A-Z]+" );
+ private final static Pattern chromosome_PATTERN = Pattern.compile( "\\s+/chromosome=\"(\\w+)\"" );
+ private final static Pattern map_PATTERN = Pattern.compile( "\\s+/map=\"([\\w\\.]+)\"" );
+ private final static Pattern gene_PATTERN = Pattern.compile( "\\s+/gene=\"(.+)\"" );
+ private final static Pattern mim_PATTERN = Pattern.compile( "\\s+/db_xref=\"MIM:(\\d+)\"" );
+ private final static Pattern taxon_PATTERN = Pattern.compile( "\\s+/db_xref=\"taxon:(\\d+)\"" );
+ private final static Pattern interpro_PATTERN = Pattern.compile( "\\s+/db_xref=\"InterPro:([A-Z0-9]+)\"" );
+ private final static Pattern uniprot_PATTERN = Pattern.compile( "\\s+/db_xref=\"UniProtKB/[A-Za-z-]*:(\\w+)\"" );
+ private final static Pattern hgnc_PATTERN = Pattern.compile( "\\s+/db_xref=\"[A-Z:]*HGNC:(\\d+)\"" );
+ private final static Pattern geneid_PATTERN = Pattern.compile( "\\s+/db_xref=\"GeneID:(\\d+)\"" );
+ private final static Pattern pdb_PATTERN = Pattern.compile( "\\s+/db_xref=\"PDB:([A-Z0-9]+)\"" );
+ private final static Pattern ec_PATTERN = Pattern.compile( "\\s+/EC_number=\"([\\.\\-\\d]+)\"" );
+ private final static Pattern product_PATTERN = Pattern.compile( "\\s+/product=\"(\\w{1,10})\"" );
+
private SortedSet<Annotation> _annotations;
private String _chromosome;
private SortedSet<Accession> _cross_references;
private String _gene_name;
private String _map;
private String _os;
- // FIXME actually this is NCBI entry
- //http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/emb/AAR37336/
private String _pa;
private String _provider;
private String _symbol;
private String _tax_id;
-
- // TODO PUBMED 15798186
- //TODO (FEATURES)
- // source /db_xref="taxon:9606"
- // gene 1..2881
- // /gene="RBM39"
- //
- // /db_xref="MIM:604739"
- // CDS
- // /gene="RBM39"
- // /db_xref="MIM:604739"
- // /db_xref="InterPro:IPR002475"
- // /product="Bcl-2"
- // /db_xref="UniProtKB/TrEMBL:Q5J7V1" <- reparse?
- //
- // Protein
- /*
- LOCUS NM_184234 2881 bp mRNA linear PRI 16-JUN-2013
- DEFINITION Homo sapiens RNA binding motif protein 39 (RBM39), transcript
- variant 1, mRNA.
- ACCESSION NM_184234
- VERSION NM_184234.2 GI:336176061
- KEYWORDS RefSeq.
- SOURCE Homo sapiens (human)
- ORGANISM Homo sapiens
- Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
- Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
- Catarrhini; Hominidae; Homo.
- REFERENCE 1 (bases 1 to 2881)
- AUTHORS Sillars-Hardebol,A.H., Carvalho,B., Belien,J.A., de Wit,M.,
- Delis-van Diemen,P.M., Tijssen,M., van de Wiel,M.A., Ponten,F.,
- Meijer,G.A. and Fijneman,R.J.
- TITLE CSE1L, DIDO1 and RBM39 in colorectal adenoma to carcinoma
- progression
- JOURNAL Cell Oncol (Dordr) 35 (4), 293-300 (2012)
- PUBMED 22711543
- REMARK GeneRIF: Data show that CSE1L, DIDO1 and RBM39 mRNA expression
- levels correlated with chromosome 20q DNA copy number status.
- REFERENCE 2 (bases 1 to 2881)
- AUTHORS Huang,G., Zhou,Z., Wang,H. and Kleinerman,E.S.
- TITLE CAPER-alpha alternative splicing regulates the expression of
- vascular endothelial growth factor(1)(6)(5) in Ewing sarcoma cells
- JOURNAL Cancer 118 (8), 2106-2116 (2012)
- PUBMED 22009261
- REMARK GeneRIF: Increased VEGF(165) expression is secondary to the
- down-regulation of CAPER-alpha by EWS/FLI-1. CAPER-alpha mediates
- alternative splicing and controls the shift from VEGF(189) to
- VEGF(165) .
- REFERENCE 3 (bases 1 to 2881)
- AUTHORS Han,B., Stockwin,L.H., Hancock,C., Yu,S.X., Hollingshead,M.G. and
- Newton,D.L.
- TITLE Proteomic analysis of nuclei isolated from cancer cell lines
- treated with indenoisoquinoline NSC 724998, a novel topoisomerase I
- inhibitor
- JOURNAL J. Proteome Res. 9 (8), 4016-4027 (2010)
- PUBMED 20515076
- REMARK Erratum:[J Proteome Res. 2011 Apr 1;10(4):2128]
- REFERENCE 4 (bases 1 to 2881)
- AUTHORS Zhang,J.Y., Looi,K.S. and Tan,E.M.
- TITLE Identification of tumor-associated antigens as diagnostic and
- predictive biomarkers in cancer
- JOURNAL Methods Mol. Biol. 520, 1-10 (2009)
- PUBMED 19381943
- REFERENCE 5 (bases 1 to 2881)
- AUTHORS Dutta,J., Fan,G. and Gelinas,C.
- TITLE CAPERalpha is a novel Rel-TAD-interacting factor that inhibits
- lymphocyte transformation by the potent Rel/NF-kappaB oncoprotein
- v-Rel
- JOURNAL J. Virol. 82 (21), 10792-10802 (2008)
- PUBMED 18753212
- REMARK GeneRIF: this study identifies CAPERalpha (RNA binding motif
- protein 39) as a new transcriptional coregulator for v-Rel and
- reveals an important role in modulating Rel's oncogenic activity.
- REFERENCE 6 (bases 1 to 2881)
- AUTHORS Cazalla,D., Newton,K. and Caceres,J.F.
- TITLE A novel SR-related protein is required for the second step of
- Pre-mRNA splicing
- JOURNAL Mol. Cell. Biol. 25 (8), 2969-2980 (2005)
- PUBMED 15798186
- REFERENCE 7 (bases 1 to 2881)
- AUTHORS Dowhan,D.H., Hong,E.P., Auboeuf,D., Dennis,A.P., Wilson,M.M.,
- Berget,S.M. and O'Malley,B.W.
- TITLE Steroid hormone receptor coactivation and alternative RNA splicing
- by U2AF65-related proteins CAPERalpha and CAPERbeta
- JOURNAL Mol. Cell 17 (3), 429-439 (2005)
- PUBMED 15694343
- REFERENCE 8 (bases 1 to 2881)
- AUTHORS Sun,N.N., Fastje,C.D., Wong,S.S., Sheppard,P.R., Macdonald,S.J.,
- Ridenour,G., Hyde,J.D. and Witten,M.L.
- TITLE Dose-dependent transcriptome changes by metal ores on a human acute
- lymphoblastic leukemia cell line
- JOURNAL Toxicol Ind Health 19 (7-10), 157-163 (2003)
- PUBMED 15747776
- REMARK GeneRIF: 10 genes were down-regulated following treatment of the
- T-ALL cells with 0.15 and 1.5 microg/mL of metal ores at 72 h
- REFERENCE 9 (bases 1 to 2881)
- AUTHORS Jung,D.J., Na,S.Y., Na,D.S. and Lee,J.W.
- TITLE Molecular cloning and characterization of CAPER, a novel
- coactivator of activating protein-1 and estrogen receptors
- JOURNAL J. Biol. Chem. 277 (2), 1229-1234 (2002)
- PUBMED 11704680
- REMARK GeneRIF: This paper describes the mouse gene.
- REFERENCE 10 (bases 1 to 2881)
- AUTHORS Imai,H., Chan,E.K., Kiyosawa,K., Fu,X.D. and Tan,E.M.
- TITLE Novel nuclear autoantigen with splicing factor motifs identified
- with antibody from hepatocellular carcinoma
- JOURNAL J. Clin. Invest. 92 (5), 2419-2426 (1993)
- PUBMED 8227358
- COMMENT REVIEWED REFSEQ: This record has been curated by NCBI staff. The
- reference sequence was derived from DC346351.1, BC141835.1 and
- C75555.1.
- On Jun 16, 2011 this sequence version replaced gi:35493810.
-
- Summary: This gene encodes a member of the U2AF65 family of
- proteins. The encoded protein is found in the nucleus, where it
- co-localizes with core spliceosomal proteins. It has been shown to
- play a role in both steroid hormone receptor-mediated transcription
- and alternative splicing, and it is also a transcriptional
- coregulator of the viral oncoprotein v-Rel. Multiple transcript
- variants have been observed for this gene. A related pseudogene has
- been identified on chromosome X. [provided by RefSeq, Aug 2011].
-
- Transcript Variant: This variant (1) encodes the longest isoform
- (a, also called CC1.4).
-
- Publication Note: This RefSeq record includes a subset of the
- publications that are available for this gene. Please see the Gene
- record to access additional publications.
-
- ##Evidence-Data-START##
- Transcript exon combination :: BC141835.1, L10911.1 [ECO:0000332]
- RNAseq introns :: mixed/partial sample support
- ERS025081, ERS025082 [ECO:0000350]
- ##Evidence-Data-END##
- COMPLETENESS: complete on the 3' end.
- PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
- 1-578 DC346351.1 3-580
- 579-2872 BC141835.1 429-2722
- 2873-2881 C75555.1 1-9 c
- FEATURES Location/Qualifiers
- source 1..2881
- /organism="Homo sapiens"
- /mol_type="mRNA"
- /db_xref="taxon:9606"
- /chromosome="20"
- /map="20q11.22"
- gene 1..2881
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /note="RNA binding motif protein 39"
- /db_xref="GeneID:9584"
- /db_xref="HGNC:15923"
- /db_xref="HPRD:09201"
- /db_xref="MIM:604739"
- exon 1..396
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /inference="alignment:Splign:1.39.8"
- STS 35..262
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /standard_name="REN58946"
- /db_xref="UniSTS:383746"
- misc_feature 221..223
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /note="upstream in-frame stop codon"
- STS 299..453
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /standard_name="G64285"
- /db_xref="UniSTS:158667"
- exon 397..460
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /inference="alignment:Splign:1.39.8"
- CDS 410..2002
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /note="isoform a is encoded by transcript variant 1;
- coactivator of activating protein-1 and estrogen
- receptors; functional spliceosome-associated protein 59;
- RNA-binding region (RNP1, RRM) containing 2;
- hepatocellular carcinoma protein 1; splicing factor HCC1"
- /codon_start=1
- /product="RNA-binding protein 39 isoform a"
- /protein_id="NP_909122.1"
- /db_xref="GI:35493811"
- /db_xref="CCDS:CCDS13266.1"
- /db_xref="GeneID:9584"
- /db_xref="HGNC:15923"
- /db_xref="HPRD:09201"
- /db_xref="MIM:604739"
- /translation="MADDIDIEAMLEAPYKKDENKLSSANGHEERSKKRKKSKSRSRS
- HERKRSKSKERKRSRDRERKKSKSRERKRSRSKERRRSRSRSRDRRFRGRYRSPYSGP
- KFNSAIRGKIGLPHSIKLSRRRSRSKSPFRKDKSPVREPIDNLTPEERDARTVFCMQL
- AARIRPRDLEEFFSTVGKVRDVRMISDRNSRRSKGIAYVEFVDVSSVPLAIGLTGQRV
- LGVPIIVQASQAEKNRAAAMANNLQKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRI
- ESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPMKVGHVTERTDASS
- ASSFLDSDELERTGIDLGTTGRLQLMARLAEGTGLQIPPAAQQALQMSGSLAFGAVAE
- FSFVIDLQTRLSQQTEASALAAAASVQPLATQCFQLSNMFNPQTEEEVGWDTEIKDDV
- IEECNKHGGVIHIYVDKNSAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITAAYVPL
- PTYHNLFPDSMTATQLLVPSRR"
- misc_feature 413..415
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /experiment="experimental evidence, no additional details
- recorded"
- /note="N-acetylalanine; propagated from
- UniProtKB/Swiss-Prot (Q14498.2); acetylation site"
-
- exon 461..510
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /inference="alignment:Splign:1.39.8"
-
- exon 1902..2874
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /inference="alignment:Splign:1.39.8"
- STS 1956..2182
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /standard_name="REN58786"
- /db_xref="UniSTS:383586"
- STS 2104..2148
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /standard_name="D19S1033"
- /db_xref="UniSTS:154759"
- STS 2145..2400
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- /standard_name="REN58785"
- /db_xref="UniSTS:383585"
-
- polyA_signal 2851..2856
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- polyA_site 2874
- /gene="RBM39"
- /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
- ORIGIN
- 1 atttggagct tggggcagct tctcgcgaga gcccgtgctg agggctctgt gaggccccgt
- 61 gtgtttgtgt gtgtgtatgt gtgctggtga atgtgagtac agggaagcag cggccgccat
- 121 ttcagggagc ttgtcgacgc tgtcgcaggg gtggatcctg agctgccgaa gccgccgtcc
- 181 tgctctcccg cgtgggcttc tctaattcca ttgttttttt tagattctct cgggcctagc
- 241 cgtccttgga acccgatatt cgggctgggc ggttccgcgg cctgggccta ggggcttaac
-
-
-
- */
+
private EbiDbEntry() {
}
&& ForesterUtil.isEmpty( getTaxonomyIdentifier() ) && ForesterUtil.isEmpty( getSequenceSymbol() ) );
}
- public void setProvider( final String provider ) {
- _provider = provider;
- }
+ @Override
+ public MolecularSequence getMolecularSequence() {
+ // TODO Auto-generated method stub
+ return null;
+ }
private void addAnnotation( final Annotation annotation ) {
if ( _annotations == null ) {
_annotations = new TreeSet<Annotation>();
_os = os;
}
}
-
- // public static SequenceDatabaseEntry createInstanceFromPlainText( final List<String> lines ) {
- // final EbiDbEntry e = new EbiDbEntry();
- // for( final String line : lines ) {
- // if ( line.startsWith( "PA" ) ) {
- // e.setPA( SequenceDbWsTools.extractFrom( line, "PA" ) );
- // }
- // else if ( line.startsWith( "DE" ) ) {
- // e.setDe( SequenceDbWsTools.extractFrom( line, "DE" ) );
- // }
- // else if ( line.startsWith( "OS" ) ) {
- // if ( line.indexOf( "(" ) > 0 ) {
- // e.setOs( SequenceDbWsTools.extractFromTo( line, "OS", "(" ) );
- // }
- // else {
- // e.setOs( SequenceDbWsTools.extractFrom( line, "OS" ) );
- // }
- // }
- // else if ( line.startsWith( "OX" ) ) {
- // if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
- // e.setTaxId( SequenceDbWsTools.extractFromTo( line, "NCBI_TaxID=", ";" ) );
- // }
- // }
- // }
- // return e;
- // }
- public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List<String> lines ) {
- final Pattern X_PATTERN = Pattern.compile( "^[A-Z]+" );
- final Pattern chromosome_PATTERN = Pattern.compile( "\\s+/chromosome=\"(\\w+)\"" );
- final Pattern map_PATTERN = Pattern.compile( "\\s+/map=\"([\\w+\\.])\"" );
- final Pattern gene_PATTERN = Pattern.compile( "\\s+/gene=\"(.+)\"" );
- final Pattern mim_PATTERN = Pattern.compile( "\\s+/db_xref=\"MIM:(\\d+)\"" );
- final Pattern taxon_PATTERN = Pattern.compile( "\\s+/db_xref=\"taxon:(\\d+)\"" );
- final Pattern interpro_PATTERN = Pattern.compile( "\\s+/db_xref=\"InterPro:([A-Z0-9]+)\"" );
- final Pattern uniprot_PATTERN = Pattern.compile( "\\s+/db_xref=\"UniProtKB/[A-Za-z-]*:(\\w+)\"" );
- final Pattern hgnc_PATTERN = Pattern.compile( "\\s+/db_xref=\"[A-Z:]*HGNC:(\\d+)\"" );
- final Pattern geneid_PATTERN = Pattern.compile( "\\s+/db_xref=\"GeneID:(\\d+)\"" );
- final Pattern pdb_PATTERN = Pattern.compile( "\\s+/db_xref=\"PDB:([A-Z0-9]+)\"" );
- final Pattern ec_PATTERN = Pattern.compile( "\\s+/EC_number=\"([\\.\\-\\d]+)\"" );
- final Pattern product_PATTERN = Pattern.compile( "\\s+/product=\"(\\w{1,10})\"" );
+
+ private static void append( final StringBuilder sb, final String s ) {
+ if ( sb.length() > 0 ) {
+ sb.append( " " );
+ }
+ sb.append( s.trim() );
+ }
+
+ public final static SequenceDatabaseEntry createInstance( final List<String> lines ) {
+
final EbiDbEntry e = new EbiDbEntry();
final StringBuilder def = new StringBuilder();
boolean in_definition = false;
}
if ( line.indexOf( "[" ) > 0 ) {
if ( definiton ) {
- x( def, ( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "[" ) ) );
+ append( def, ( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "[" ) ) );
}
else {
- x( def, ( SequenceDbWsTools.extractFromTo( line, "DE", "[" ) ) );
+ append( def, ( SequenceDbWsTools.extractFromTo( line, "DE", "[" ) ) );
}
}
else if ( line.indexOf( "." ) > 0 ) {
if ( definiton ) {
- x( def, ( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "." ) ) );
+ append( def, ( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "." ) ) );
}
else {
- x( def, ( SequenceDbWsTools.extractFromTo( line, "DE", "." ) ) );
+ append( def, ( SequenceDbWsTools.extractFromTo( line, "DE", "." ) ) );
}
}
else {
if ( definiton ) {
- x( def, ( SequenceDbWsTools.extractFrom( line, "DEFINITION" ) ) );
+ append( def, ( SequenceDbWsTools.extractFrom( line, "DEFINITION" ) ) );
}
else {
- x( def, ( SequenceDbWsTools.extractFrom( line, "DE" ) ) );
+ append( def, ( SequenceDbWsTools.extractFrom( line, "DE" ) ) );
}
}
if ( definiton ) {
else {
e.setTaxonomyScientificName( SequenceDbWsTools.extractFrom( line, " ORGANISM" ) );
}
- // in_def = false;
}
else if ( line.startsWith( "OS " ) ) {
if ( line.indexOf( "(" ) > 0 ) {
else {
in_definition = false;
}
- if ( !line.startsWith( "FT " ) && X_PATTERN.matcher( line ).find() ) {
+ if ( !line.startsWith( "FT " ) && LETTERS_PATTERN.matcher( line ).find() ) {
in_features = false;
in_source = false;
in_gene = false;
in_cds = false;
in_mrna = false;
in_protein = false;
- // in_def = false;
}
if ( line.startsWith( "FEATURES " ) || line.startsWith( "FT " ) ) {
in_features = true;
return e;
}
- private static void x( final StringBuilder sb, final String s ) {
- if ( sb.length() > 0 ) {
- sb.append( " " );
- }
- sb.append( s.trim() );
- }
-
- @Override
- public MolecularSequence getMolecularSequence() {
- // TODO Auto-generated method stub
- return null;
- }
}
git://source.jalview.org / jalview.git / commitdiff