From 2800c6cab99546cb62e2e792ee3af32b856b092b Mon Sep 17 00:00:00 2001 From: idoerg Date: Fri, 18 Feb 2005 05:16:22 +0000 Subject: [PATCH] *** empty log message *** --- Bio/Blast/NCBIWWW.py | 4 +- Tests/output/test_NCBIWWW | 1748 ------------------------------------ Tests/output/test_Registry | 4 +- Tests/test_Registry.py | 36 +- setup.py | 2 +- 5 files changed, 22 insertions(+), 1772 deletions(-) diff --git a/Bio/Blast/NCBIWWW.py b/Bio/Blast/NCBIWWW.py index 9d7a1b5f1cd..cbf147dc55d 100644 --- a/Bio/Blast/NCBIWWW.py +++ b/Bio/Blast/NCBIWWW.py @@ -315,7 +315,7 @@ def _scan_alignments(self, uhandle, consumer): is_pairwise = is_masterslave = 0 # Was line1, changed to line2. 16-feb-2005. Iddo -# if string.find(line2, 'Alignments') >= 0: +# if string.find(line1, 'Alignments') >= 0: if string.find(line2, 'Alignments') >= 0: is_pairwise = 1 elif line2[:10] == ' Database': @@ -327,7 +327,7 @@ def _scan_alignments(self, uhandle, consumer): elif line1[:5] == '
':
             is_pairwise = 1
         else:
-            raise SyntaxError, "Cannot resolve location at line:\n%s\n%s" % (line1, line2)
+            raise SyntaxError, "Cannot resolve location at lines:\n%s\n%s" % (line1, line2)
 
         if is_pairwise:
             self._scan_pairwise_alignments(uhandle, consumer)
diff --git a/Tests/output/test_NCBIWWW b/Tests/output/test_NCBIWWW
index 0fad5735797..3845feac13c 100644
--- a/Tests/output/test_NCBIWWW
+++ b/Tests/output/test_NCBIWWW
@@ -21,1751 +21,3 @@ Running tests on _Scanner
 ************************************************** TESTING bt037
 ************************************************** TESTING bt038
 ************************************************** TESTING bt061
-************************************************** TESTING bt064
-************************************************** TESTING bt066
-************************************************** TESTING bt069
-************************************************** TESTING bt070
-************************************************** TESTING bt019
-noevent        : 
-noevent        : 
-noevent        : BLAST Search Results 
-noevent        : 
-noevent        :  
-*************** start_header
-version        : BLASTP 2.0.10 [Aug-26-1999]
-noevent        : 
-noevent        : 
-reference      : Reference
-reference      : Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäf
-reference      : Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1
-reference      : "Gapped BLAST and PSI-BLAST: a new generation of protein databa
-reference      : programs",  Nucleic Acids Res. 25:3389-3402.
-noevent        : 

-query_info     : Query= gi|120291|sp|P21297|FLBT_CAUCR FLBT PROTEIN.
-query_info     :          (141 letters)
-noevent        : 
-database_info  : Database: Non-redundant SwissProt sequences
-database_info  :            82,258 sequences; 29,652,561 total letters
-noevent        : 
-noevent        : 
 
If you have any problems or questions with the results o
-noevent        : 

-noevent        : 

-noevent        : 

-noevent        : 
 Distri
-noevent        : 
-noevent        : 

-noevent        : 
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :   
-*************** start_header
-version        : BLASTP 2.0.10 [Aug-26-1999]
-noevent        : 
-noevent        : 
-reference      : Reference
-reference      : Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäf
-reference      : Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1
-reference      : "Gapped BLAST and PSI-BLAST: a new generation of protein databa
-reference      : programs",  Nucleic Acids Res. 25:3389-3402.
-noevent        : 

-query_info     : Query= gi|132349|sp|P15394|REPA_AGRTU REPLICATING PROTEI
-query_info     :          (250 letters)
-noevent        : 
-database_info  : Database: Non-redundant SwissProt sequences
-database_info  :            82,258 sequences; 29,652,561 total letters
-noevent        : 
-noevent        : 
 
If you have any problems or questions with the results o
-noevent        : 
-noevent        : 

-noevent        : 

-noevent        : 
 Distri
-noevent        : 
-noevent        : 

-noevent        : 
-multalign      : blast_tmp 1    MFQQIGAVQAKSGTDEPAHPCEKFPPERKCEAVFWKPLPRHEAREILL
-multalign      : 
-noevent        : 
-*************** end_alignment
-*************** start_database_report
-noevent        : 
-database       :   Database: Non-redundant SwissProt sequences
-posted_date    :     Posted date:  Dec 18, 1999  8:26 PM
-num_letters_in_:   Number of letters in database: 29,652,561
-num_sequences_i:   Number of sequences in database:  82,258
-noevent        : 
-noevent        : Lambda     K      H
-ka_params      :    0.317    0.133    0.395
-noevent        : 
-gapped         : Gapped
-noevent        : Lambda     K      H
-ka_params_gap  :    0.270   0.0470    0.230
-noevent        : 
-noevent        : 
-*************** end_database_report
-*************** start_parameters
-matrix         : Matrix: BLOSUM62
-gap_penalties  : Gap Penalties: Existence: 11, Extension: 1
-num_hits       : Number of Hits to DB: 14679054
-num_sequences  : Number of Sequences: 82258
-num_extends    : Number of extensions: 599117
-num_good_extend: Number of successful extensions: 1508
-num_seqs_better: Number of sequences better than 10.0: 15
-hsps_no_gap    : Number of HSP's better than 10.0 without gapping: 4
-hsps_prelim_gap: Number of HSP's successfully gapped in prelim test: 11
-hsps_prelim_gap: Number of HSP's that attempted gapping in prelim test: 1504
-hsps_gapped    : Number of HSP's gapped (non-prelim): 15
-query_length   : length of query: 250
-database_length: length of database: 29,652,561
-effective_hsp_l: effective HSP length: 51
-effective_query: effective length of query: 199
-effective_datab: effective length of database: 25,457,403
-effective_searc: effective search space: 5066023197
-effective_searc: effective search space used: 5066023197
-threshold      : T: 11
-window_size    : A: 40
-dropoff_1st_pas: X1: 16 ( 7.3 bits)
-gap_x_dropoff  : X2: 38 (14.8 bits)
-gap_x_dropoff_f: X3: 64 (24.9 bits)
-gap_trigger    : S1: 41 (21.7 bits)
-blast_cutoff   : S2: 63 (29.0 bits)
-noevent        : 
-noevent        : 

-*************** end_parameters
-noevent        : 
-noevent        : 
-noevent        : 
-noevent        : 
-noevent        : 
-************************************************** TESTING bt026
-noevent        : 
-noevent        : 
-noevent        : BLAST Search Results 
-noevent        : 
-noevent        :  
-*************** start_header
-version        : BLASTN 2.0.10 [Aug-26-1999]
-noevent        : 
-noevent        : 
-reference      : Reference
-reference      : Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäf
-reference      : Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1
-reference      : "Gapped BLAST and PSI-BLAST: a new generation of protein databa
-reference      : programs",  Nucleic Acids Res. 25:3389-3402.
-noevent        : 

-query_info     : Query= gi|1347201|gb|G24969.1|G24969 human STS EST21946.
-query_info     :          (331 letters)
-noevent        : 
-database_info  : Database: Non-redundant Database of GenBank STS Division
-database_info  :            89,405 sequences; 32,867,852 total letters
-noevent        : 
-noevent        : 
 
If you have any problems or questions with the results o
-noevent        : 
-noevent        : 

-noevent        : 

-noevent        : 
 Distri
-noevent        : 
-noevent        : 

-noevent        : 
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_database_report
-noevent        : 
-database       :   Database: Non-redundant Database of GenBank STS Division
-posted_date    :     Posted date:  Dec 18, 1999  7:45 PM
-num_letters_in_:   Number of letters in database: 32,867,852
-num_sequences_i:   Number of sequences in database:  89,405
-noevent        : 
-noevent        : Lambda     K      H
-ka_params      :     1.37    0.711     1.31
-noevent        : 
-gapped         : Gapped
-noevent        : Lambda     K      H
-ka_params_gap  :     1.37    0.711     1.31
-noevent        : 
-noevent        : 
-*************** end_database_report
-*************** start_parameters
-matrix         : Matrix: blastn matrix:1 -3
-gap_penalties  : Gap Penalties: Existence: 5, Extension: 2
-num_hits       : Number of Hits to DB: 7042
-num_sequences  : Number of Sequences: 89405
-num_extends    : Number of extensions: 7042
-num_good_extend: Number of successful extensions: 1951
-num_seqs_better: Number of sequences better than 10.0: 13
-query_length   : length of query: 331
-database_length: length of database: 32,867,852
-effective_hsp_l: effective HSP length: 17
-effective_query: effective length of query: 314
-effective_datab: effective length of database: 31,347,967
-effective_searc: effective search space: 9843261638
-effective_searc: effective search space used: 9843261638
-threshold      : T: 0
-window_size    : A: 0
-dropoff_1st_pas: X1: 6 (11.9 bits)
-gap_x_dropoff  : X2: 10 (19.8 bits)
-gap_trigger    : S1: 12 (24.3 bits)
-blast_cutoff   : S2: 15 (30.2 bits)
-noevent        : 
-noevent        : 

-*************** end_parameters
-noevent        : 
-noevent        : 
-noevent        : 
-noevent        : 
-noevent        : 
-************************************************** TESTING bt028
-noevent        : 
-noevent        : 
-noevent        : BLAST Search Results 
-noevent        : 
-noevent        :  
-*************** start_header
-version        : BLASTX 2.0.10 [Aug-26-1999]
-noevent        : 
-noevent        : 
-reference      : Reference
-reference      : Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäf
-reference      : Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1
-reference      : "Gapped BLAST and PSI-BLAST: a new generation of protein databa
-reference      : programs",  Nucleic Acids Res. 25:3389-3402.
-noevent        : 

-query_info     : Query= gi|1347369|gb|G25137.1|G25137 human STS EST48004.
-query_info     :          (556 letters)
-noevent        : 
-database_info  : Database: Non-redundant SwissProt sequences
-database_info  :            82,258 sequences; 29,652,561 total letters
-noevent        : 
-noevent        : 
 
If you have any problems or questions with the results o
-noevent        : 
-noevent        : 

-noevent        : 

-noevent        : 
 Distri
-noevent        : 
-noevent        : 

-noevent        : 
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** start_hsp
-noevent        : 
-score          :  Score = 31.3 bits (69), Expect = 1.5
-identities     :  Identities = 18/50 (36%), Positives = 26/50 (52%)
-frame          :  Frame = +1
-noevent        : 
-query          : Query: 1   DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQ 1
-align          :            DL  L +++  FP GT  RW+ IA+ +         R+  DV  KAK L+
-sbjct          : Sbjct: 332 DLSQLTRSMVKFPGGTPGRWDKIAHELG--------RSVTDVTTKAKELK 3
-noevent        : 

-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :   
-*************** start_header
-version        : TBLASTN 2.0.10 [Aug-26-1999]
-noevent        : 
-noevent        : 
-reference      : Reference
-reference      : Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäf
-reference      : Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1
-reference      : "Gapped BLAST and PSI-BLAST: a new generation of protein databa
-reference      : programs",  Nucleic Acids Res. 25:3389-3402.
-noevent        : 

-query_info     : Query= gi|729325|sp|P39483|DHG2_BACME GLUCOSE 1-DEHYDROG
-query_info     : II (GLCDH-II).
-query_info     :          (261 letters)
-noevent        : 
-database_info  : Database: Non-redundant Database of GenBank STS Division
-database_info  :            89,405 sequences; 32,867,852 total letters
-noevent        : 
-noevent        : 
 
If you have any problems or questions with the results o
-noevent        : 
-noevent        : 

-noevent        : 

-noevent        : 
 Distri
-noevent        : 
-noevent        : 

-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :   
-*************** start_header
-version        : TBLASTX 2.0.10 [Aug-26-1999]
-noevent        : 
-noevent        : 
-reference      : Reference
-reference      : Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäf
-reference      : Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1
-reference      : "Gapped BLAST and PSI-BLAST: a new generation of protein databa
-reference      : programs",  Nucleic Acids Res. 25:3389-3402.
-noevent        : 

-query_info     : Query= gi|1348853|gb|G26621.1|G26621 human STS STS_D1200
-query_info     :          (615 letters)
-noevent        : 
-database_info  : Database: Non-redundant Database of GenBank STS Division
-database_info  :            89,526 sequences; 32,906,604 total letters
-noevent        : 
-noevent        : 
 
If you have any problems or questions with the results o
-noevent        : 
-noevent        : 

-noevent        : 

-noevent        : 
 Distri
-noevent        : 
-noevent        : 

-noevent        : 
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** start_hsp
-noevent        : 
-score          :  Score =  340 bits (736), Expect = 9e-94
-identities     :  Identities = 204/204 (100%), Positives = 204/204 (100%)
-frame          :  Frame = +3 / +3
-noevent        : 
-noevent        : 
-query          : Query: 3   SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*
-align          :            SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*
-sbjct          : Sbjct: 3   SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*
-noevent        : 
-noevent        : 
-query          : Query: 183 IGYFKPALFFM*PVLPHLLSSF*PLLNFLLYSHCSGGQIT*VLQILAGKIYS
-align          :            IGYFKPALFFM*PVLPHLLSSF*PLLNFLLYSHCSGGQIT*VLQILAGKIYS
-sbjct          : Sbjct: 183 IGYFKPALFFM*PVLPHLLSSF*PLLNFLLYSHCSGGQIT*VLQILAGKIYS
-noevent        : 
-noevent        : 
-query          : Query: 363 PKMDFQSWLHMALXXSY*XXXGFLXFRSXGQRWQIXGVXXWXGXLXXXXFXG
-align          :            PKMDFQSWLHMAL  SY*   GFL FRS GQRWQI GV  W G L    F G
-sbjct          : Sbjct: 363 PKMDFQSWLHMALXXSY*XXXGFLXFRSXGQRWQIXGVXXWXGXLXXXXFXG
-noevent        : 
-noevent        : 
-query          : Query: 543 SXXVGAXGXXXFXXXGXXXXXXXW 614
-align          :            S  VGA G   F   G       W
-sbjct          : Sbjct: 543 SXXVGAXGXXXFXXXGXXXXXXXW 614
-noevent        : 

-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** start_hsp
-noevent        : 
-score          :  Score =  350 bits (759), Expect = 6e-97
-identities     :  Identities = 195/205 (95%), Positives = 195/205 (95%)
-frame          :  Frame = +1 / +1
-noevent        : 
-noevent        : 
-query          : Query: 1   DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCT
-align          :            DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCT
-sbjct          : Sbjct: 1   DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCT
-noevent        : 
-noevent        : 
-query          : Query: 181 A*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYT
-align          :            A*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYT
-sbjct          : Sbjct: 181 A*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYT
-noevent        : 
-noevent        : 
-query          : Query: 361 ILKWISKAGYTWPWXXXIXFXXAFFXXXXXXXXXXXXXXLXGXVX*XXXXSX
-align          :            ILKWISKAGYTWPW   I F  AFF              L G V *    S
-sbjct          : Sbjct: 361 ILKWISKAGYTWPWXXXIXFXXAFFXSGVXVNGGKSXGXLXGXVX*XXXXSX
-noevent        : 
-noevent        : 
-query          : Query: 541 XPXGWVXXGXFXFXXXXXXFXXXLG 615
-align          :             P GWV  G F F      F   LG
-sbjct          : Sbjct: 541 XPXGWVXXGXFXFXXXXXXFXXXLG 615
-noevent        : 

-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** start_hsp
-noevent        : 
-score          :  Score =  398 bits (864), Expect = e-111
-identities     :  Identities = 205/205 (100%), Positives = 205/205 (100%)
-frame          :  Frame = -1 / -1
-noevent        : 
-noevent        : 
-query          : Query: 615 PKXXXKXXXXXXKTKXTXXHPPXWXXNXXXLWPXXXXXXLXNXXX*XPXGFA
-align          :            PK   K      KTK T  HPP W  N   LWP      L N   * P GFA
-sbjct          : Sbjct: 615 PKXXXKXXXXXXKTKXTXXHPPXWXXNXXXLWPXXXXXXLXNXXX*XPXGFA
-noevent        : 
-noevent        : 
-query          : Query: 435 EESPXKXNXTXPGPCVTSFGNPF*DYXSAXS*CCIFFLPGFGVPRLFVHQNN
-align          :            EESP K N T PGPCVTSFGNPF*DY SA S*CCIFFLPGFGVPRLFVHQNN
-sbjct          : Sbjct: 435 EESPXKXNXTXPGPCVTSFGNPF*DYXSAXS*CCIFFLPGFGVPRLFVHQNN
-noevent        : 
-noevent        : 
-query          : Query: 255 VVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRF
-align          :            VVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRF
-sbjct          : Sbjct: 255 VVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRF
-noevent        : 
-noevent        : 
-query          : Query: 75  LCIHSHFSCQSGQNEESHEWRGILI 1
-align          :            LCIHSHFSCQSGQNEESHEWRGILI
-sbjct          : Sbjct: 75  LCIHSHFSCQSGQNEESHEWRGILI 1
-noevent        : 

-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** start_hsp
-noevent        : 
-score          :  Score =  390 bits (846), Expect = e-109
-identities     :  Identities = 196/196 (100%), Positives = 196/196 (100%)
-frame          :  Frame = -3 / -3
-noevent        : 
-noevent        : 
-query          : Query: 589 PXXXNXXNPXAPTXXXX*PXPPXAPXKXXXXXXPXXLXTPXICHR*PKLLKX
-align          :            P   N  NP APT    *P PP AP K      P  L TP ICHR*PKLLK
-sbjct          : Sbjct: 589 PXXXNXXNPXAPTXXXX*PXPPXAPXKXXXXXXPXXLXTPXICHR*PKLLKX
-noevent        : 
-noevent        : 
-query          : Query: 409 DXXRAMCNQLWKSILGLXECXFIMLYIFPARIWST*VICPPEQWL*RRKLSS
-align          :            D  RAMCNQLWKSILGL EC FIMLYIFPARIWST*VICPPEQWL*RRKLSS
-sbjct          : Sbjct: 409 DXXRAMCNQLWKSILGLXECXFIMLYIFPARIWST*VICPPEQWL*RRKLSS
-noevent        : 
-noevent        : 
-query          : Query: 229 GKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRA
-align          :            GKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRA
-sbjct          : Sbjct: 229 GKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRA
-noevent        : 
-noevent        : 
-query          : Query: 49  SKWTK*RVS*VEGHSD 2
-align          :            SKWTK*RVS*VEGHSD
-sbjct          : Sbjct: 49  SKWTK*RVS*VEGHSD 2
-noevent        : 

-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** start_hsp
-noevent        : 
-score          :  Score =  281 bits (608), Expect = 4e-76
-identities     :  Identities = 122/122 (100%), Positives = 122/122 (100%)
-frame          :  Frame = -2 / -2
-noevent        : 
-noevent        : 
-query          : Query: 368 FRIT*VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLH
-align          :            FRIT*VL HNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLH
-sbjct          : Sbjct: 368 FRIT*VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLH
-noevent        : 
-noevent        : 
-query          : Query: 188 TYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKM
-align          :            TYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKM
-sbjct          : Sbjct: 188 TYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKM
-noevent        : 
-noevent        : 
-query          : Query: 8   F* 3
-align          :            F*
-sbjct          : Sbjct: 8   F* 3
-noevent        : 

-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  
-noevent        : 
-noevent        : 
-*************** end_hsp
-*************** end_alignment
-*************** start_alignment
-noevent        : 
-title          :  = 0, \
-                    (swissprot_location.name, first_line)
+#    def t_swissprot(self):
+#        """Retrieval of Swissprot records from various sources.
+#        """
+#        sp_db = db["swissprot"]
+#        for swissprot_location in sp_db.objs:
+#            handle = swissprot_location[self.sp_id]
+#            first_line = handle.read(20)
+#            assert first_line.find(self.sp_id) >= 0, \
+#                    (swissprot_location.name, first_line)
 
     def t_embl(self):
         """Retrieval of EMBL records from various sources.
@@ -103,15 +103,15 @@ def t_interpro(self):
             assert data.find(self.interpro_id) >= 0, \
                     (interpro_location.name, data)
 
-    def t_pdb(self):
-        """Retrieval of PDB data from various locations.
-        """
-        pdb_db = db["pdb"]
-        for pdb_loc in pdb_db.objs:
-            handle = pdb_loc[self.pdb_id]
-            first_line = handle.read(80)
-            assert first_line.find(self.pdb_id) >= 0, \
-                    (pdb_loc.name, first_line)
+#    def t_pdb(self):
+#        """Retrieval of PDB data from various locations.
+#        """
+#        pdb_db = db["pdb"]
+#        for pdb_loc in pdb_db.objs:
+#            handle = pdb_loc[self.pdb_id]
+#            first_line = handle.read(80)
+#            assert first_line.find(self.pdb_id) >= 0, \
+#                    (pdb_loc.name, first_line)
 
     def t_prodoc(self):
         """Retrieval of Prodoc data from various locations.
diff --git a/setup.py b/setup.py
index f42285ff82a..ef57575f79e 100644
--- a/setup.py
+++ b/setup.py
@@ -434,7 +434,7 @@ def is_reportlab_installed():
               include_dirs=["Bio"],
               libraries=["fl"]
               ),
-    Extension('Bio.cnexus',
+    Extension('Bio.Nexus.cnexus',
               ['Bio/Nexus/cnexus.c']
               ),
     Extension('Bio.Restriction.DNAUtils',