import java.util.Locale;
import java.util.Set;
import java.util.SortedSet;
-import java.util.TreeSet;
import org.forester.application.support_transfer;
import org.forester.archaeopteryx.TreePanelUtil;
@SuppressWarnings( "unused")
public final class Test {
+ private final static boolean PERFORM_DB_TESTS = true;
private final static double ZERO_DIFF = 1.0E-9;
private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" )
+ ForesterUtil.getFileSeparator() + "test_data"
System.out.println( "failed." );
failed++;
}
- System.out.print( "Sequence DB tools 2: " );
- if ( testSequenceDbWsTools2() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- System.exit( -1 );
+ if ( PERFORM_DB_TESTS ) {
+ System.out.print( "Sequence DB tools 2: " );
+ if ( testSequenceDbWsTools2() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ System.exit( -1 );
+ }
}
System.exit( 0 );
System.out.print( "Hmmscan output parser: " );
System.out.println( "failed." );
failed++;
}
- System.out.print( "Uniprot Entry Retrieval: " );
- if ( Test.testUniprotEntryRetrieval() ) {
- System.out.println( "OK." );
- succeeded++;
- }
- else {
- System.out.println( "failed." );
- failed++;
- }
- System.out.print( "Uniprot Taxonomy Search: " );
- if ( Test.testUniprotTaxonomySearch() ) {
- System.out.println( "OK." );
- succeeded++;
+ if ( PERFORM_DB_TESTS ) {
+ System.out.print( "Uniprot Entry Retrieval: " );
+ if ( Test.testUniprotEntryRetrieval() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
}
- else {
- System.out.println( "failed." );
- failed++;
+ if ( PERFORM_DB_TESTS ) {
+ System.out.print( "Uniprot Taxonomy Search: " );
+ if ( Test.testUniprotTaxonomySearch() ) {
+ System.out.println( "OK." );
+ succeeded++;
+ }
+ else {
+ System.out.println( "failed." );
+ failed++;
+ }
}
//----
String path = "";
private static boolean testSequenceDbWsTools1() {
try {
- PhylogenyNode n = new PhylogenyNode();
+ final PhylogenyNode n = new PhylogenyNode();
n.setName( "NP_001025424" );
Accession acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.REFSEQ.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
|| !acc.getValue().equals( "NP_001025424" ) ) {
return false;
}
n.setName( "340 0559 -- _NP_001025424_dsfdg15 05" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.REFSEQ.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
|| !acc.getValue().equals( "NP_001025424" ) ) {
return false;
}
n.setName( "NP_001025424.1" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.REFSEQ.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
|| !acc.getValue().equals( "NP_001025424" ) ) {
return false;
}
n.setName( "NM_001030253" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.REFSEQ.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.REFSEQ.toString() )
|| !acc.getValue().equals( "NM_001030253" ) ) {
return false;
}
n.setName( "BCL2_HUMAN" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.UNIPROT.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
|| !acc.getValue().equals( "BCL2_HUMAN" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "P10415" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.UNIPROT.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
|| !acc.getValue().equals( "P10415" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( " P10415 " );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.UNIPROT.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
|| !acc.getValue().equals( "P10415" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "_P10415|" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.UNIPROT.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.UNIPROT.toString() )
|| !acc.getValue().equals( "P10415" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "AY695820" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.NCBI.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
|| !acc.getValue().equals( "AY695820" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "_AY695820_" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.NCBI.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
|| !acc.getValue().equals( "AY695820" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "AAA59452" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.NCBI.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
|| !acc.getValue().equals( "AAA59452" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "_AAA59452_" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.NCBI.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
|| !acc.getValue().equals( "AAA59452" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "AAA59452.1" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.NCBI.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
|| !acc.getValue().equals( "AAA59452.1" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "_AAA59452.1_" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.NCBI.toString() )
+ if ( ( acc == null ) || !acc.getSource().equals( Source.NCBI.toString() )
|| !acc.getValue().equals( "AAA59452.1" ) ) {
System.out.println( acc.toString() );
return false;
}
n.setName( "GI:94894583" );
acc = SequenceDbWsTools.obtainSeqAccession( n );
- if ( acc == null || !acc.getSource().equals( Source.GI.toString() ) || !acc.getValue().equals( "94894583" ) ) {
+ if ( ( acc == null ) || !acc.getSource().equals( Source.GI.toString() )
+ || !acc.getValue().equals( "94894583" ) ) {
System.out.println( acc.toString() );
return false;
}
private static boolean testSequenceDbWsTools2() {
try {
- PhylogenyNode n1 = new PhylogenyNode();
- n1.setName( "NP_001025424" );
- SequenceDbWsTools.obtainSeqInformation( false, 4000, new TreeSet<String>(), n1 );
+ final PhylogenyNode n1 = new PhylogenyNode( "NP_001025424" );
+ SequenceDbWsTools.obtainSeqInformation( n1 );
if ( !n1.getNodeData().getSequence().getName().equals( "Bcl2" ) ) {
return false;
}
if ( !n1.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
return false;
}
- PhylogenyNode n2 = new PhylogenyNode();
- n2.setName( "NM_001030253" );
- SequenceDbWsTools.obtainSeqInformation( false, 4000, new TreeSet<String>(), n2 );
+ if ( !n1.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+ return false;
+ }
+ if ( !n1.getNodeData().getSequence().getAccession().getValue().equals( "NP_001025424" ) ) {
+ return false;
+ }
+ final PhylogenyNode n2 = new PhylogenyNode( "NM_001030253" );
+ SequenceDbWsTools.obtainSeqInformation( n2 );
System.out.println( n2.toString() );
if ( !n2.getNodeData().getSequence().getName()
.equals( "Danio rerio B-cell leukemia/lymphoma 2 (bcl2), mRNA" ) ) {
if ( !n2.getNodeData().getTaxonomy().getScientificName().equals( "Danio rerio" ) ) {
return false;
}
+ if ( !n2.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+ return false;
+ }
+ if ( !n2.getNodeData().getSequence().getAccession().getValue().equals( "NM_001030253" ) ) {
+ return false;
+ }
+ final PhylogenyNode n3 = new PhylogenyNode( "NM_184234.2" );
+ SequenceDbWsTools.obtainSeqInformation( n3 );
+ System.out.println( "n=" + n3.toString() );
+ if ( !n3.getNodeData().getSequence().getName()
+ .equals( "Homo sapiens RNA binding motif protein 39 (RBM39), transcript variant 1, mRNA" ) ) {
+ return false;
+ }
+ if ( !n3.getNodeData().getTaxonomy().getScientificName().equals( "Homo sapiens" ) ) {
+ return false;
+ }
+ if ( !n3.getNodeData().getSequence().getAccession().getSource().equals( Source.REFSEQ.toString() ) ) {
+ return false;
+ }
+ if ( !n3.getNodeData().getSequence().getAccession().getValue().equals( "NM_184234" ) ) {
+ return false;
+ }
}
catch ( final IOException e ) {
System.out.println();
return true;
}
catch ( final Exception e ) {
+ e.printStackTrace();
return false;
}
return true;
public final class EbiDbEntry implements SequenceDatabaseEntry {
+ // FIXME actually this is NCBI entry
//http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/emb/AAR37336/
private String _pa;
private String _de;
private String _symbol;
private String _provider;
+ // 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"
+ // /protein_id="NP_909122.1"
+ // /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"
+ misc_feature 692..694
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="Phosphotyrosine; propagated from
+ UniProtKB/Swiss-Prot (Q14498.2); phosphorylation site"
+ misc_feature 698..700
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
+ (Q14498.2); phosphorylation site"
+ misc_feature 707..709
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
+ (Q14498.2); phosphorylation site"
+ misc_feature 815..817
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
+ (Q14498.2); phosphorylation site"
+ misc_feature 845..847
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="Phosphothreonine; propagated from
+ UniProtKB/Swiss-Prot (Q14498.2); phosphorylation site"
+ misc_feature 1280..1627
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="non-experimental evidence, no additional
+ details recorded"
+ /note="propagated from UniProtKB/Swiss-Prot (Q14498.2);
+ Region: Interaction with JUN (By similarity)"
+ misc_feature 1280..1474
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="non-experimental evidence, no additional
+ details recorded"
+ /note="propagated from UniProtKB/Swiss-Prot (Q14498.2);
+ Region: Activating domain (By similarity)"
+ misc_feature 1409..1411
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
+ (Q14498.2); phosphorylation site"
+ misc_feature 1418..1420
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
+ (Q14498.2); phosphorylation site"
+ misc_feature 1430..1432
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /experiment="experimental evidence, no additional details
+ recorded"
+ /note="Phosphoserine; propagated from UniProtKB/Swiss-Prot
+ (Q14498.2); phosphorylation site"
+ misc_feature 1472..1627
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="non-experimental evidence, no additional
+ details recorded"
+ /note="propagated from UniProtKB/Swiss-Prot (Q14498.2);
+ Region: Interaction with ESR1 and ESR2 (By similarity)"
+ misc_feature 1625..1999
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="non-experimental evidence, no additional
+ details recorded"
+ /note="propagated from UniProtKB/Swiss-Prot (Q14498.2);
+ Region: Interaction with NCOA6 (By similarity)"
+ exon 461..510
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 511..705
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 706..771
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 772..825
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 826..943
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 944..1096
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 1097..1234
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 1235..1300
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 1301..1505
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 1506..1583
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 1584..1634
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 1635..1716
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 1717..1822
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /inference="alignment:Splign:1.39.8"
+ exon 1823..1901
+ /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"
+ STS 2349..2590
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="REN58784"
+ /db_xref="UniSTS:383584"
+ STS 2450..2669
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="RH69003"
+ /db_xref="UniSTS:85360"
+ STS 2579..2828
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="REN58783"
+ /db_xref="UniSTS:383583"
+ STS 2639..2728
+ /gene="RBM39"
+ /gene_synonym="CAPER; CAPERalpha; FSAP59; HCC1; RNPC2"
+ /standard_name="RH67917"
+ /db_xref="UniSTS:84037"
+ 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
+ 301 agtagcaaca gaagcggcgg cggcggcagc agcagcagca gcagcagcaa tctcttcccg
+ 361 aacacgagca ccacaggcgc ccgaaggccg gaacaggcgt ttagagaaaa tggcagacga
+ 421 tattgatatt gaagcaatgc ttgaggctcc ttacaagaag gatgagaaca agttgagcag
+ 481 tgccaacggc catgaagaac gtagcaaaaa gaggaaaaaa agcaagagca gaagtcgtag
+ 541 tcatgaacga aagagaagca aaagtaagga acggaagcga agtagagaca gagaaaggaa
+ 601 aaagagcaaa agccgtgaaa gaaagcgaag tagaagcaaa gagaggcgac ggagccgctc
+ 661 aagaagtcga gatcgaagat ttagaggccg ctacagaagt ccttactccg gaccaaaatt
+ 721 taacagtgcc atccgaggaa agattgggtt gcctcatagc atcaaattaa gcagacgacg
+ 781 ttcccgaagc aaaagtccat tcagaaaaga caagagccct gtgagagaac ctattgataa
+ 841 tttaactcct gaggaaagag atgcaaggac agtcttctgt atgcagctgg cggcaagaat
+ 901 tcgaccaagg gatttggaag agtttttctc tacagtagga aaggttcgag atgtgaggat
+ 961 gatttctgac agaaattcaa gacgttccaa aggaattgct tatgtggagt tcgtcgatgt
+ 1021 tagctcagtg cctctagcaa taggattaac tggccaacga gttttaggcg tgccaatcat
+ 1081 agtacaggca tcacaggcag aaaaaaacag agctgcagca atggcaaaca atttacaaaa
+ 1141 gggaagtgct ggacctatga ggctttatgt gggctcatta cacttcaaca taactgaaga
+ 1201 tatgcttcgt gggatctttg agccttttgg aagaattgaa agtatccagc tgatgatgga
+ 1261 cagtgaaact ggtcgatcca agggatatgg atttattaca ttttctgact cagaatgtgc
+ 1321 caaaaaggct ttggaacaac ttaatggatt tgaactagca ggaagaccaa tgaaagttgg
+ 1381 tcatgttact gaacgtactg atgcttcgag tgctagttca tttttggaca gtgatgaact
+ 1441 ggaaaggact ggaattgatt tgggaacaac tggtcgtctt cagttaatgg caagacttgc
+ 1501 agagggtaca ggtttgcaga ttccgccagc agcacagcaa gctctacaga tgagtggctc
+ 1561 tttggcattt ggtgctgtgg cagaattctc ttttgttata gatttgcaaa caagactttc
+ 1621 ccagcagact gaagcttcag ctttagctgc agctgcctct gttcagccac ttgcaacaca
+ 1681 atgtttccaa ctctctaaca tgtttaaccc tcaaacagaa gaagaagttg gatgggatac
+ 1741 cgagattaag gatgatgtga ttgaagaatg taataaacat ggaggagtta ttcatattta
+ 1801 tgttgacaaa aattcagctc agggcaatgt gtatgtgaag tgcccatcaa ttgctgcagc
+ 1861 tattgctgct gtcaatgcat tgcatggcag gtggtttgct ggtaaaatga taacagcagc
+ 1921 atatgtacct cttccaactt accacaacct gtttcctgat tctatgacag caacacagct
+ 1981 actggttcca agtagacgat gaaggaagat atagtccctt atgtatatag ctttttttct
+ 2041 ttcttgagaa ttcatcttga gttatctttt atttagataa aaataaagag gcaaggatct
+ 2101 actgtcattt gtatgcaatt tcctgttacc ttgaaaaaat aaaaatgtta acaggaatgc
+ 2161 agtgtgctca ttctccctaa atagtaaatc ccactgtata caaaactgtt ctcttgttct
+ 2221 gccttttaaa atgttcatgt agaaaattaa tgaactatag gaatagctct aggagaacaa
+ 2281 atgtgctttc tgtaaaaagg cagaccaggg atgtaatgtt tttaatgttt cagaagccta
+ 2341 actttttaca cagtggttac atttcacatt tcactaatgt tgatatttgg ctgatggttg
+ 2401 agcagtttct gaaatacaca tttagtgtat ggaaatacaa gacagctaaa gggctgtttg
+ 2461 gttagcatct catcttgcat tctgatcaat tggcaagaaa gggagatttc aaaattatat
+ 2521 ttcttgatgg tatcttttca attaatgtat ctgtaaaagt ttctttgtaa atactatgtg
+ 2581 ttctggtgtg tcttaaaatt ccaaacaaaa tgatccctgc atttcctgaa gatgtttaaa
+ 2641 cgtgagagtc tggtaggcaa agcagtctga gaaagaaata ggaaatgcag aaataggttt
+ 2701 tgtctggttg catataatct ttgctctttt taagctctgt gagctctgaa atatattttt
+ 2761 gggttacttc agtgtgtttg acaagacagc ttgatatttc tatcaaacaa atgactttca
+ 2821 tattgcaaca atctttgtaa gaaccactca aataaaagtc tcttaaaaag gccaaaaaaa
+ 2881 a
+
+
+ */
private EbiDbEntry() {
}
public static SequenceDatabaseEntry createInstanceFromPlainTextForRefSeq( final List<String> lines ) {
final EbiDbEntry e = new EbiDbEntry();
+ final StringBuilder def = new StringBuilder();
+ boolean in_def = false;
for( final String line : lines ) {
// System.out.println( "-" + line );
if ( line.startsWith( "ACCESSION" ) ) {
- e.setPA( DatabaseTools.extract( line, "ACCESSION" ) );
+ e.setPA( SequenceDbWsTools.extractFrom( line, "ACCESSION" ) );
+ in_def = false;
}
else if ( line.startsWith( "DEFINITION" ) ) {
if ( line.indexOf( "[" ) > 0 ) {
- e.setDe( DatabaseTools.extract( line, "DEFINITION", "[" ) );
+ def.append( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "[" ) );
}
else if ( line.indexOf( "." ) > 0 ) {
- e.setDe( DatabaseTools.extract( line, "DEFINITION", "." ) );
+ def.append( SequenceDbWsTools.extractFromTo( line, "DEFINITION", "." ) );
}
else {
- e.setDe( DatabaseTools.extract( line, "DEFINITION" ) );
+ def.append( SequenceDbWsTools.extractFrom( line, "DEFINITION" ) );
}
+ in_def = true;
}
else if ( line.startsWith( "SOURCE" ) ) {
if ( line.indexOf( "(" ) > 0 ) {
- e.setOs( DatabaseTools.extract( line, "SOURCE", "(" ) );
+ e.setOs( SequenceDbWsTools.extractFromTo( line, "SOURCE", "(" ) );
}
else {
- e.setOs( DatabaseTools.extract( line, "SOURCE" ) );
+ e.setOs( SequenceDbWsTools.extractFrom( line, "SOURCE" ) );
}
+ in_def = false;
}
+ else if ( line.startsWith( " " ) && in_def ) {
+ def.append( " " );
+ if ( line.indexOf( "[" ) > 0 ) {
+ def.append( SequenceDbWsTools.extractTo( line, "[" ) );
+ }
+ else if ( line.indexOf( "." ) > 0 ) {
+ def.append( SequenceDbWsTools.extractTo( line, "." ) );
+ }
+ else {
+ def.append( line.trim() );
+ }
+ }
+ else {
+ in_def = false;
+ }
+ }
+ if ( def.length() > 0 ) {
+ e.setDe( def.toString().trim() );
}
return e;
}
final EbiDbEntry e = new EbiDbEntry();
for( final String line : lines ) {
if ( line.startsWith( "PA" ) ) {
- e.setPA( DatabaseTools.extract( line, "PA" ) );
+ e.setPA( SequenceDbWsTools.extractFrom( line, "PA" ) );
}
else if ( line.startsWith( "DE" ) ) {
- e.setDe( DatabaseTools.extract( line, "DE" ) );
+ e.setDe( SequenceDbWsTools.extractFrom( line, "DE" ) );
}
else if ( line.startsWith( "OS" ) ) {
if ( line.indexOf( "(" ) > 0 ) {
- e.setOs( DatabaseTools.extract( line, "OS", "(" ) );
+ e.setOs( SequenceDbWsTools.extractFromTo( line, "OS", "(" ) );
}
else {
- e.setOs( DatabaseTools.extract( line, "OS" ) );
+ e.setOs( SequenceDbWsTools.extractFrom( line, "OS" ) );
}
}
else if ( line.startsWith( "OX" ) ) {
if ( line.indexOf( "NCBI_TaxID=" ) > 0 ) {
- e.setTaxId( DatabaseTools.extract( line, "NCBI_TaxID=", ";" ) );
+ e.setTaxId( SequenceDbWsTools.extractFromTo( line, "NCBI_TaxID=", ";" ) );
}
}
}
git://source.jalview.org / jalview.git / commitdiff