Question: (Closed) Parse Blast Output ..
0
gravatar for Suraj
6.2 years ago by
Suraj0
Suraj0 wrote:

i want to parse this blast output but compilers giving NULLPOINTEREXCEPTION .. input file and source code of java program is given below ... plz help me out..

Exception in thread "main" java.lang.NullPointerException
    at org.biojava.bio.program.sax.BlastSAXParser.interpret(BlastSAXParser.java:224)
    at org.biojava.bio.program.sax.BlastSAXParser.parse(BlastSAXParser.java:168)
    at org.biojava.bio.program.sax.BlastLikeSAXParser.onNewDataSet(BlastLikeSAXParser.java:314)
    at org.biojava.bio.program.sax.BlastLikeSAXParser.interpret(BlastLikeSAXParser.java:276)
    at org.biojava.bio.program.sax.BlastLikeSAXParser.parse(BlastLikeSAXParser.java:163)

source code

 public static void main(String[] args) throws IOException 
    {     
        //BioJava bio=new BioJava();
      //  NewClass newClass = new NewClass();
      try {


      //get the Blast input as a Stream
      InputStream is = new FileInputStream(args[0]);

      //make a BlastLikeSAXParser
      BlastLikeSAXParser parser = new BlastLikeSAXParser();


      // try to parse, even if the blast version is not recognized.
      parser.setModeLazy();


      //make the SAX event adapter that will pass events to a Handler.
      SeqSimilarityAdapter adapter = new SeqSimilarityAdapter();

      //set the parsers SAX event adapter
      parser.setContentHandler(adapter);

      //The list to hold the SeqSimilaritySearchResults
      ArrayList results = new ArrayList();

      //create the SearchContentHandler that will build SeqSimilaritySearchResults
      //in the results List
      SearchContentHandler builder = new BlastLikeSearchBuilder(results,   new DummySequenceDB("queries"), new DummySequenceDBInstallation());

      //register builder with adapter
      adapter.setSearchContentHandler(builder);

      //parse the file, after this the result List will be populated with
      //SeqSimilaritySearchResults
      parser.parse(new InputSource(is));

      //output some blast details
      for (Iterator i = results.iterator(); i.hasNext(); )
      {
          SeqSimilaritySearchResult result =(SeqSimilaritySearchResult)i.next();

        Annotation anno = result.getAnnotation();

        for (Iterator j = anno.keys().iterator(); j.hasNext(); )
        {
          Object key = j.next();
          Object property = anno.getProperty(key);
          System.out.println(key+" : "+property);
        }
        System.out.println("Hits: ");

        //list the hits
        for (Iterator k = result.getHits().iterator(); k.hasNext(); )
        {
          SeqSimilaritySearchHit hit =(SeqSimilaritySearchHit)k.next();
          System.out.print("\tmatch: "+hit.getSubjectID());System.out.println("\te score: "+hit.getEValue());
        }

        System.out.println("\n");
      }

    }
    catch (SAXException ex) {
      //XML problem
    }catch (IOException ex) {
      //IO problem, possibly file not found
    }         
    }

input file

BLASTP 2.2.12 [Aug-07-2005]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.

Query= gi|7290941|gb|AAF46381.1| (AE003444) CG15351 gene product
[Drosophila melanogaster]
         (308 letters)

Database: drosoph.aa 
           14,331 sequences; 7,178,856 total letters



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gb|AAF46381.1| (AE003444) CG15351 gene product [Drosophila melan...   530   e-151
gb|AAF47693.1| (AE003476) CG9973 gene product [Drosophila melano...    31   0.66 
gb|AAF48598.1| (AE003502) CG18734 gene product [alt 1] [Drosophi...    30   1.5  
gb|AAF48599.1| (AE003502) CG18734 gene product [alt 2] [Drosophi...    30   1.5  
gb|AAF52676.1| (AE003621) D12 gene product [Drosophila melanogas...    29   1.9  
gb|AAF50352.1| (AE003553) CG5735 gene product [alt 1] [Drosophil...    29   2.5  
gb|AAF50350.1| (AE003553) CG5735 gene product [alt 2] [Drosophil...    29   2.5  
gb|AAF50351.1| (AE003553) CG5735 gene product [alt 3] [Drosophil...    29   2.5  
gb|AAF58433.1| (AE003820) Su(z)2 gene product [Drosophila melano...    28   3.3  
gb|AAF54698.1| (AE003693) CG17360 gene product [Drosophila melan...    28   3.3  
gb|AAF46511.1| (AE003447) CG3003 gene product [Drosophila melano...    28   3.3  
gb|AAF51348.2| (AE003585) CG17660 gene product [Drosophila melan...    28   4.3  
gb|AAF58741.1| (AE003828) CG7701 gene product [Drosophila melano...    28   5.6  
gb|AAF46218.1| (AE003439) CG14432 gene product [Drosophila melan...    28   5.6  
gb|AAF59227.1| (AE003840) blow gene product [Drosophila melanoga...    27   7.3  
gb|AAF56314.1| (AE003748) CG13624 gene product [Drosophila melan...    27   7.3  
gb|AAF50413.1| (AE003555) Gug gene product [Drosophila melanogas...    27   7.3  
gb|AAF47179.1| (AE003463) CG3363 gene product [Drosophila melano...    27   7.3  
gb|AAF55377.1| (AE003716) CG5225 gene product [Drosophila melano...    27   9.5  
gb|AAF51468.2| (AE003588) ds gene product [Drosophila melanogaster]    27   9.5  
gb|AAF49573.1| (AE003529) CG12712 gene product [Drosophila melan...    27   9.5  
gb|AAF49773.2| (AE003536) CG9007 gene product [Drosophila melano...    27   9.5  
gb|AAF48937.1| (AE003511) CG7884 gene product [Drosophila melano...    27   9.5  

>gb|AAF46381.1| (AE003444) CG15351 gene product [Drosophila melanogaster]
          Length = 308

 Score =  530 bits (1366), Expect = e-151
 Identities = 263/308 (85%), Positives = 263/308 (85%)

Query: 1   MLVYSSLFVQNLSESTPGPDEEYNVSTTPGAPLEETTNRLAARVEPYDKGDREQYDVIDV 60
           MLVYSSLFVQNLSESTPGPDEEYNVSTTPGAPLEETTNRLAARVEPYDKGDREQYDVIDV
Sbjct: 1   MLVYSSLFVQNLSESTPGPDEEYNVSTTPGAPLEETTNRLAARVEPYDKGDREQYDVIDV 60

Query: 61  ATATGTVMGKPRSGQTTRIYTTGEVDESFWLKHLGDDFKHAIHLQVGGTNEEYNRLINRT 120
           ATATGTVMGKPRSGQTTRIYTTGEVDESFWLKHLGDDFKHAIHLQVGGTNEEYNRLINRT
Sbjct: 61  ATATGTVMGKPRSGQTTRIYTTGEVDESFWLKHLGDDFKHAIHLQVGGTNEEYNRLINRT 120

Query: 121 QNGVHEEVHHEYLPGAERPGSAVQPPSPLPAPHQSRPAYRQGFDNRAMAMKQQYLIHXXX 180
           QNGVHEEVHHEYLPGAERPGSAVQPPSPLPAPHQSRPAYRQGFDNRAMAMKQQYLIH   
Sbjct: 121 QNGVHEEVHHEYLPGAERPGSAVQPPSPLPAPHQSRPAYRQGFDNRAMAMKQQYLIHQQT 180

Query: 181 XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXRNTYAMPQNYGQQNYKPQ 240
                                                     RNTYAMPQNYGQQNYKPQ
Sbjct: 181 QQSHPAQQRYNYAQQHAQHYAPQPQLQPQPQPQPQYPQHTPHRNTYAMPQNYGQQNYKPQ 240

Query: 241 SYIINSSEDQLHAEQSNPSPMKSAGEDRQHHEEEFDSFGGQLNFKSPFNDYGSRPARDLT 300
           SYIINSSEDQLHAEQSNPSPMKSAGEDRQHHEEEFDSFGGQLNFKSPFNDYGSRPARDLT
Sbjct: 241 SYIINSSEDQLHAEQSNPSPMKSAGEDRQHHEEEFDSFGGQLNFKSPFNDYGSRPARDLT 300

Query: 301 YLLYKRGL 308
           YLLYKRGL
Sbjct: 301 YLLYKRGL 308


>gb|AAF47693.1| (AE003476) CG9973 gene product [Drosophila melanogaster]
          Length = 697

 Score = 30.8 bits (68), Expect = 0.66
 Identities = 11/48 (22%), Positives = 26/48 (54%)

Query: 224 NTYAMPQNYGQQNYKPQSYIINSSEDQLHAEQSNPSPMKSAGEDRQHH 271
           ++++ P ++ QQ+Y  Q ++    + Q HA+Q +    +   + +Q H
Sbjct: 60  HSHSHPHHHYQQHYPQQQHLQQQQQQQHHAQQQHQQQQQQQQQQQQQH 107


>gb|AAF48598.1| (AE003502) CG18734 gene product [alt 1] [Drosophila melanogaster]
          Length = 1679

 Score = 29.6 bits (65), Expect = 1.5
 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 235 QNYKPQSYIINSSEDQLHAEQSNPSPMKSAGEDRQHHEE----EFDSFGGQLNFKSPFND 290
           Q  + +S ++NSS        SNP    SA    Q   E      DSF   LN+++ F+ 
Sbjct: 852 QPMRLKSELLNSSPQLRSPSSSNPFLFPSASNIGQPANEGGNFNTDSFASYLNYQNIFSS 911

Query: 291 YGSRP 295
            GS P
Sbjct: 912 AGSDP 916


>gb|AAF48599.1| (AE003502) CG18734 gene product [alt 2] [Drosophila melanogaster]
          Length = 1679

 Score = 29.6 bits (65), Expect = 1.5
 Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 235 QNYKPQSYIINSSEDQLHAEQSNPSPMKSAGEDRQHHEE----EFDSFGGQLNFKSPFND 290
           Q  + +S ++NSS        SNP    SA    Q   E      DSF   LN+++ F+ 
Sbjct: 852 QPMRLKSELLNSSPQLRSPSSSNPFLFPSASNIGQPANEGGNFNTDSFASYLNYQNIFSS 911

Query: 291 YGSRP 295
            GS P
Sbjct: 912 AGSDP 916


>gb|AAF52676.1| (AE003621) D12 gene product [Drosophila melanogaster]
          Length = 969

 Score = 29.3 bits (64), Expect = 1.9
 Identities = 20/61 (32%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 234 QQNYKPQSYIINSSEDQL-HAEQSNPSPMKSAGED----RQHHEEEFDSFGGQLNFKSPF 288
           QQ  K Q  + + S+D+    EQ  P  +K   E     RQ HE + +    +LN K+ F
Sbjct: 190 QQKIKEQGIVTDHSKDKKDQPEQEPPISVKLEDEQPCTSRQAHERQVELNASRLNNKNKF 249

Query: 289 N 289
           N
Sbjct: 250 N 250


>gb|AAF50352.1| (AE003553) CG5735 gene product [alt 1] [Drosophila melanogaster]
          Length = 551

 Score = 28.9 bits (63), Expect = 2.5
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 229 PQNYGQQNYKP-QSYIINSSEDQLHAEQSNPSPMKSAGEDRQHHEEEFDSFGGQLNFKSP 287
           PQ + QQ+ +  Q +  +  + QLH  Q   SP  SA       +++    GG  +  SP
Sbjct: 22  PQLHQQQHQQQHQQHQQHQQQQQLHQHQQQLSPNLSALHHHHQQQQQLRESGGSHSPSSP 81

Query: 288 FNDYGSRP 295
               G  P
Sbjct: 82  GGGGGGSP 89


>gb|AAF50350.1| (AE003553) CG5735 gene product [alt 2] [Drosophila melanogaster]
          Length = 704

 Score = 28.9 bits (63), Expect = 2.5
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 229 PQNYGQQNYKP-QSYIINSSEDQLHAEQSNPSPMKSAGEDRQHHEEEFDSFGGQLNFKSP 287
           PQ + QQ+ +  Q +  +  + QLH  Q   SP  SA       +++    GG  +  SP
Sbjct: 175 PQLHQQQHQQQHQQHQQHQQQQQLHQHQQQLSPNLSALHHHHQQQQQLRESGGSHSPSSP 234

Query: 288 FNDYGSRP 295
               G  P
Sbjct: 235 GGGGGGSP 242


>gb|AAF50351.1| (AE003553) CG5735 gene product [alt 3] [Drosophila melanogaster]
          Length = 704

 Score = 28.9 bits (63), Expect = 2.5
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 229 PQNYGQQNYKP-QSYIINSSEDQLHAEQSNPSPMKSAGEDRQHHEEEFDSFGGQLNFKSP 287
           PQ + QQ+ +  Q +  +  + QLH  Q   SP  SA       +++    GG  +  SP
Sbjct: 175 PQLHQQQHQQQHQQHQQHQQQQQLHQHQQQLSPNLSALHHHHQQQQQLRESGGSHSPSSP 234

Query: 288 FNDYGSRP 295
               G  P
Sbjct: 235 GGGGGGSP 242


>gb|AAF58433.1| (AE003820) Su(z)2 gene product [Drosophila melanogaster]
          Length = 1368

 Score = 28.5 bits (62), Expect = 3.3
 Identities = 38/191 (19%), Positives = 68/191 (35%), Gaps = 43/191 (22%)

Query: 10  QNLSESTPGPDEEYNVSTTPGAPLEETTNRLAARVEPYDKGDREQYDVIDVATATGTVMG 69
           Q L +S   PD +Y+ + +P +    +TN           G        D +T+T T   
Sbjct: 448 QPLQQSASNPDSKYSPNASPMSSCSSSTN-----------GSSSSLGTADASTSTSTSSS 496

Query: 70  ------------KPRSGQTTRIYT--TGEVDESFWLKHLGD-----DFKHAIHLQVGGTN 110
                       K  +G+  +++   + + D    +K         DFK +  L  G  +
Sbjct: 497 HRKRKKKHSKEPKDANGKRKKLHAEISSQTDGKMKVKITAKPNHKLDFKRSHSLASGELD 556

Query: 111 EEYNRL--------INRTQNGVHEEVHHEYLPGAERPGSAVQPPSPLPAPHQSRPAYRQG 162
            +  +L        +NRT       ++   + GA  P     PP+P   P Q +   +Q 
Sbjct: 557 LQKLKLDSTSTSEALNRTLGEEARSINSLVVGGAPTP-----PPTPTAEPEQQQQQQQQQ 611

Query: 163 FDNRAMAMKQQ 173
              +    +QQ
Sbjct: 612 QQPQQQQQQQQ 622


>gb|AAF54698.1| (AE003693) CG17360 gene product [Drosophila melanogaster]
          Length = 1354

 Score = 28.5 bits (62), Expect = 3.3
 Identities = 13/42 (30%), Positives = 22/42 (52%)

Query: 8   FVQNLSESTPGPDEEYNVSTTPGAPLEETTNRLAARVEPYDK 49
           FV N+ E     +E+   S+T  +P+E   + +  R E +DK
Sbjct: 441 FVHNVDEQLRHKNEDDGASSTEASPMESKQSLMLHRQEEFDK 482


>gb|AAF46511.1| (AE003447) CG3003 gene product [Drosophila melanogaster]
          Length = 837

 Score = 28.5 bits (62), Expect = 3.3
 Identities = 31/144 (21%), Positives = 54/144 (37%), Gaps = 15/144 (10%)

Query: 32  PLEETTNRLAARVEPYDKGDREQYDVIDVATATGTVMGKPRSGQTTRIYTTGEVDESFWL 91
           PLE +    A   +   +GD  Q+D++D        M +           T  V      
Sbjct: 255 PLERSWPPRAVGRDLKLQGDVFQFDILDTDERLAEEMAQGSGSSNNSPLATPPVR----- 309

Query: 92  KHLGDDFKHAIHLQVGGTNEEYNRLINRTQNGVHEEVHHEYLPGAERPGSAVQPPSPLPA 151
                 FK  +  ++G   + Y   I+  +  VH+       P +   GS+   P+ L  
Sbjct: 310 ------FKPLLKKKIGP--DSYINTISTQKVPVHQSYEFPTFPSSSAVGSSSSSPNSLQF 361

Query: 152 PH--QSRPAYRQGFDNRAMAMKQQ 173
           P+  Q RP  R   + +A + ++Q
Sbjct: 362 PYLRQHRPLTRALSNGKASSSEEQ 385


>gb|AAF51348.2| (AE003585) CG17660 gene product [Drosophila melanogaster]
          Length = 530

 Score = 28.1 bits (61), Expect = 4.3
 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 5/51 (9%)

Query: 46  PYDKGDREQYDVIDVATATGTVM----GKPRSGQTTRIYTTGEVDESFWLK 92
           P D+ D ++ D   VA A G  M    G P++  T+R  TT E D+  W++
Sbjct: 449 PEDEDDEDEEDQF-VADAYGVKMRGQNGTPKTSTTSRNATTTEEDDLRWVE 498


>gb|AAF58741.1| (AE003828) CG7701 gene product [Drosophila melanogaster]
          Length = 1218

 Score = 27.7 bits (60), Expect = 5.6
 Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 2/38 (5%)

Query: 246 SSEDQLHAEQSNPSPMKSAGED--RQHHEEEFDSFGGQ 281
           SS    H  + + S   S G D  R HHE++ D+ GG+
Sbjct: 146 SSHQYRHHSRVSTSSSISMGSDILRSHHEDDVDAVGGE 183


>gb|AAF46218.1| (AE003439) CG14432 gene product [Drosophila melanogaster]
          Length = 119

 Score = 27.7 bits (60), Expect = 5.6
 Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 226 YAMPQNYGQQNYKPQSYIINSSEDQLHAEQSNP---SPMKSAGEDRQHHEEEFDSFGGQ 281
           Y   Q+Y QQ ++ Q       + QL  +Q      +P  +  + +Q HEE+ D    Q
Sbjct: 37  YQQQQHY-QQQFQQQQQQQQQQQQQLQQQQQQQQHLTPTAALAQQQQQHEEQIDLLSTQ 94


>gb|AAF59227.1| (AE003840) blow gene product [Drosophila melanogaster]
          Length = 644

 Score = 27.3 bits (59), Expect = 7.3
 Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 5/43 (11%)

Query: 5   SSLFVQNLSESTPGPDE-----EYNVSTTPGAPLEETTNRLAA 42
           SS+ +  L E +  P       EY+V   P  PL++T++R+A+
Sbjct: 355 SSMVLPKLPEKSNSPSALARRFEYDVPKCPAQPLQDTSSRVAS 397


>gb|AAF56314.1| (AE003748) CG13624 gene product [Drosophila melanogaster]
          Length = 814

 Score = 27.3 bits (59), Expect = 7.3
 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 3/40 (7%)

Query: 121 QNGVHEEVHHEYLPGAERPGSAVQPPSPLPAPHQSRPAYR 160
           Q    +++   + PG++   S + PP P   PH +RP Y+
Sbjct: 388 QKPQQQQLSASFSPGSQASQSPLTPPPP---PHANRPQYQ 424


>gb|AAF50413.1| (AE003555) Gug gene product [Drosophila melanogaster]
          Length = 1963

 Score = 27.3 bits (59), Expect = 7.3
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 124  VHEEVH-HEYLPGAERPGS---AVQPPSPLPAPHQSRPAYRQGFDNRAMAMKQQ 173
            +H  +H H +L G  RP     ++ P +P+P   Q  P +  G      + +QQ
Sbjct: 1052 MHPHLHPHAHLQGLHRPHDLPPSMHPHAPMPLSLQGHPQHGHGLPPSHTSQQQQ 1105


>gb|AAF47179.1| (AE003463) CG3363 gene product [Drosophila melanogaster]
          Length = 2175

 Score = 27.3 bits (59), Expect = 7.3
 Identities = 27/118 (22%), Positives = 47/118 (39%), Gaps = 5/118 (4%)

Query: 19  PDEEYNVSTTPGAPLEETTNRLAARVEPYDKGDRE--QYDVIDVATATGTVMGKPRSGQT 76
           P+ E +V    G PL+E   R    + P+    RE  ++ V  +     T+  K    Q 
Sbjct: 562 PNVELDVMPQLGRPLDEIAKRYLQHILPHHDITREWAEFSVSTLQAPPATM--KDAEEQA 619

Query: 77  TRIYTTGEVDESFWLKHLGDDFKHAIHLQVGGTNEEYNRLINRTQNGVHEEVHHEYLP 134
           ++         +F + +L +D  H +  +V   +E  +R      N + E    E LP
Sbjct: 620 SQTPAGRRKSFTFVIPYL-NDRNHILVRRVVDRSEHLDRSFKEEPNKLQEFTFREMLP 676


>gb|AAF55377.1| (AE003716) CG5225 gene product [Drosophila melanogaster]
          Length = 594

 Score = 26.9 bits (58), Expect = 9.5
 Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 1/41 (2%)

Query: 118 NRTQNGVHEEV-HHEYLPGAERPGSAVQPPSPLPAPHQSRP 157
           +++ +G H+   HH + P    P     PP P P P  S P
Sbjct: 135 HKSGHGHHDHHDHHHHHPAPPPPPPPPPPPPPPPPPPHSHP 175


>gb|AAF51468.2| (AE003588) ds gene product [Drosophila melanogaster]
          Length = 3503

 Score = 26.9 bits (58), Expect = 9.5
 Identities = 32/134 (23%), Positives = 55/134 (41%), Gaps = 12/134 (8%)

Query: 37   TNRLAARVEPYDKGDREQYDVIDVATATGTVMGKPRSGQTTRIYTTGEVDESFWLKHLGD 96
            T  ++ R EP D+  RE YD++  A   GT +   R     RI+ +   D +  +    +
Sbjct: 1152 TGEISTR-EPLDRELRELYDLVVEARDQGTPVRSAR--VPVRIHVSDVNDNAPEIADPQE 1208

Query: 97   DFKHAIHLQVGGTNEEYNRLINRTQNGVHEEVHHEYLPGAERPGS---AVQPPS-----P 148
            D       Q  GT     R ++R  +G +  + +  + G +  G    ++ P S      
Sbjct: 1209 DVVSVREEQPPGTEVVRVRAVDR-DHGQNASITYSIVKGRDSDGHGLFSIDPTSGVIRTR 1267

Query: 149  LPAPHQSRPAYRQG 162
            +   H+ R  YR G
Sbjct: 1268 VVLDHEERSIYRLG 1281


>gb|AAF49573.1| (AE003529) CG12712 gene product [Drosophila melanogaster]
          Length = 143

 Score = 26.9 bits (58), Expect = 9.5
 Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 2/57 (3%)

Query: 110 NEEYNRLINRTQNGVHEEVHHEYLPGAERPGSAVQPPSPLPAPHQSRPAYRQGFDNR 166
           N++ N   N  +    EE   +  P    P  A  PP PL  P    P +RQ   N+
Sbjct: 37  NQDTNNNNNNNKQAAFEERLVDESPSVGEPPLA--PPIPLAIPMAPAPPHRQACKNK 91


>gb|AAF49773.2| (AE003536) CG9007 gene product [Drosophila melanogaster]
          Length = 3238

 Score = 26.9 bits (58), Expect = 9.5
 Identities = 11/30 (36%), Positives = 16/30 (53%)

Query: 133  LPGAERPGSAVQPPSPLPAPHQSRPAYRQG 162
            LPG E P   ++P   +P   Q  P+Y +G
Sbjct: 1282 LPGVEAPMQTLRPDGSVPQVAQQPPSYLKG 1311


>gb|AAF48937.1| (AE003511) CG7884 gene product [Drosophila melanogaster]
          Length = 895

 Score = 26.9 bits (58), Expect = 9.5
 Identities = 33/130 (25%), Positives = 50/130 (38%), Gaps = 23/130 (17%)

Query: 51  DREQYDVIDVATATGTVMGKPRSGQTTRIYTTGEVDESFWL------------KHLGDDF 98
           + E ++  +   AT TV   P S +TT+  T         L            + LG D 
Sbjct: 561 EEEPHEQQESKLATATVTAPPNSRRTTKYLTKILATNLRELLKRERETKRLPGQGLGVDI 620

Query: 99  KHAIHLQVGGTNEEYNRLINR----TQNGVHEEVHHEYLPGAERPGSAVQPPSPLPAPHQ 154
                   G T +EYN L +R    T  G  + +  EYL       +    P+PL +  Q
Sbjct: 621 SRLQKNIDGWTEQEYNSLSHRPSTPTIRGRSKHIPSEYLT------TTTTTPAPL-SQRQ 673

Query: 155 SRPAYRQGFD 164
           S+    +GF+
Sbjct: 674 SKTTRGEGFE 683


  Database: drosoph.aa
    Posted date:  Feb 27, 2012 11:30 AM
  Number of letters in database: 7,178,856
  Number of sequences in database:  14,331

Lambda     K      H
   0.312    0.131    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,534,426
Number of Sequences: 14331
Number of extensions: 214774
Number of successful extensions: 828
Number of sequences better than 10.0: 23
Number of HSP's better than 10.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 810
Number of HSP's gapped (non-prelim): 33
length of query: 308
length of database: 7,178,856
effective HSP length: 96
effective length of query: 212
effective length of database: 5,803,080
effective search space: 1230252960
effective search space used: 1230252960
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 58 (26.9 bits)
biojava blast parser • 2.1k views
ADD COMMENTlink modified 11 months ago by Michael Dondrup43k • written 6.2 years ago by Suraj0
1

your stacktrace is not full. I'd like to see the trace in the main program.

ADD REPLYlink written 6.2 years ago by Pierre Lindenbaum106k

Hello Suraj!

We believe that this post does not fit the main topic of this site.

Cannot reproduce, no longer relevant.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 11 months ago by Michael Dondrup43k
0
gravatar for Michael Dondrup
11 months ago by
Bergen, Norway
Michael Dondrup43k wrote:

I think the problem was that the SAX parser expects XML format, but is given standard blast output format which is not XML. Otherwise, this question cannot be answered, it has become irreproducible due to the lack of a complete stack trace and source code.

ADD COMMENTlink written 11 months ago by Michael Dondrup43k
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