| Previous changeset 32:b2795652d2b4 (2013-11-25) Next changeset 34:3952ec621ea9 (2013-11-28) |
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Commit message:
Uploaded v0.0.22b, using BLAST+ 2.2.28 now |
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modified:
test-data/blastp_four_human_vs_rhodopsin.xml test-data/blastx_rhodopsin_vs_four_human.xml test-data/tblastn_four_human_vs_rhodopsin.html test-data/tblastn_four_human_vs_rhodopsin.xml tools/ncbi_blast_plus/README.rst tools/ncbi_blast_plus/ncbi_macros.xml tools/ncbi_blast_plus/ncbi_makeblastdb.xml |
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added:
tools/ncbi_blast_plus/check_no_duplicates.py |
| b |
| diff -r b2795652d2b4 -r 5402f9b0d508 test-data/blastp_four_human_vs_rhodopsin.xml --- a/test-data/blastp_four_human_vs_rhodopsin.xml Mon Nov 25 10:58:46 2013 -0500 +++ b/test-data/blastp_four_human_vs_rhodopsin.xml Thu Nov 28 08:50:15 2013 -0500 |
| [ |
| b'@@ -2,7 +2,7 @@\n <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n <BlastOutput>\n <BlastOutput_program>blastp</BlastOutput_program>\n- <BlastOutput_version>BLASTP 2.2.27+</BlastOutput_version>\n+ <BlastOutput_version>BLASTP 2.2.28+</BlastOutput_version>\n <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, 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.</BlastOutput_reference>\n <BlastOutput_db></BlastOutput_db>\n <BlastOutput_query-ID>sp|Q9BS26|ERP44_HUMAN</BlastOutput_query-ID>\n@@ -17,630 +17,649 @@\n <Parameters_filter>F</Parameters_filter>\n </Parameters>\n </BlastOutput_param>\n- <BlastOutput_iterations>\n- <Iteration>\n- <Iteration_iter-num>1</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>2</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>3</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119568</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>4</Iteration_iter-num>\n- <Iteration_query-ID>sp|Q9BS26|ERP44_HUMAN</Iteration_query-ID>\n- <Iteration_query-def>Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteratio'..b'q>\n+ <Hsp_hseq>MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGID-YTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>\n+ <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGID YT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>0</Statistics_db-num>\n+ <Statistics_db-len>0</Statistics_db-len>\n+ <Statistics_hsp-len>29</Statistics_hsp-len>\n+ <Statistics_eff-space>101761</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>24</Iteration_iter-num>\n+ <Iteration_query-ID>sp|P08100|OPSD_HUMAN</Iteration_query-ID>\n+ <Iteration_query-def>Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>\n+ <Iteration_query-len>348</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>gi|12583665|dbj|BAB21486.1|</Hit_id>\n+ <Hit_def>fresh water form rod opsin [Conger myriaster]</Hit_def>\n+ <Hit_accession>BAB21486</Hit_accession>\n+ <Hit_len>354</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>599.356</Hsp_bit-score>\n+ <Hsp_score>1544</Hsp_score>\n+ <Hsp_evalue>0</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>341</Hsp_query-to>\n+ <Hsp_hit-from>1</Hsp_hit-from>\n+ <Hsp_hit-to>342</Hsp_hit-to>\n+ <Hsp_query-frame>0</Hsp_query-frame>\n+ <Hsp_hit-frame>0</Hsp_hit-frame>\n+ <Hsp_identity>281</Hsp_identity>\n+ <Hsp_positive>314</Hsp_positive>\n+ <Hsp_gaps>1</Hsp_gaps>\n+ <Hsp_align-len>342</Hsp_align-len>\n+ <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>\n+ <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>\n+ <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +D ASAT SKTE</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>0</Statistics_db-num>\n+ <Statistics_db-len>0</Statistics_db-len>\n+ <Statistics_hsp-len>29</Statistics_hsp-len>\n+ <Statistics_eff-space>101761</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+</BlastOutput_iterations>\n+</BlastOutput>\n+\n' |
| b |
| diff -r b2795652d2b4 -r 5402f9b0d508 test-data/blastx_rhodopsin_vs_four_human.xml --- a/test-data/blastx_rhodopsin_vs_four_human.xml Mon Nov 25 10:58:46 2013 -0500 +++ b/test-data/blastx_rhodopsin_vs_four_human.xml Thu Nov 28 08:50:15 2013 -0500 |
| b |
| b'@@ -2,7 +2,7 @@\n <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n <BlastOutput>\n <BlastOutput_program>blastx</BlastOutput_program>\n- <BlastOutput_version>BLASTX 2.2.27+</BlastOutput_version>\n+ <BlastOutput_version>BLASTX 2.2.28+</BlastOutput_version>\n <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, 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.</BlastOutput_reference>\n <BlastOutput_db></BlastOutput_db>\n <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n@@ -17,706 +17,725 @@\n <Parameters_filter>L;</Parameters_filter>\n </Parameters>\n </BlastOutput_param>\n- <BlastOutput_iterations>\n- <Iteration>\n- <Iteration_iter-num>1</Iteration_iter-num>\n- <Iteration_query-ID>Query_1</Iteration_query-ID>\n- <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def>\n- <Iteration_query-len>1047</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119944</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>2</Iteration_iter-num>\n- <Iteration_query-ID>Query_1</Iteration_query-ID>\n- <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def>\n- <Iteration_query-len>1047</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119944</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>3</Iteration_iter-num>\n- <Iteration_query-ID>Query_1</Iteration_query-ID>\n- <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def>\n- <Iteration_query-len>1047</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>30</Statistics_hsp-len>\n- <Statistics_eff-space>119944</Statistics_eff-space>\n- <Statistics_kappa>0.041</Statistics_kappa>\n- <Statistics_lambda>0.267</Statistics_lambda>\n- <Statistics_entropy>0.14</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>4</Iteration_iter-num>\n- <Iteration_query-ID>Query_1</Iteration_query-ID>\n- <Iteration_query-def>gi|57163782|ref|NM_001009242.1| Felis catus rhodopsin (RHO), mRNA</Iteration_query-def>\n- <Iteration_query-len>1047</Iteration_query-len>\n- <Iteration_hits>\n- <Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>Subject_4</Hit_id>\n- <Hit_def>sp|P08100|OPS'..b'Statistics_db-len>\n+ <Statistics_hsp-len>32</Statistics_hsp-len>\n+ <Statistics_eff-space>155584</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+ <Iteration_message>No hits found</Iteration_message>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>23</Iteration_iter-num>\n+ <Iteration_query-ID>Query_6</Iteration_query-ID>\n+ <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def>\n+ <Iteration_query-len>1344</Iteration_query-len>\n+<Iteration_hits>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>0</Statistics_db-num>\n+ <Statistics_db-len>0</Statistics_db-len>\n+ <Statistics_hsp-len>32</Statistics_hsp-len>\n+ <Statistics_eff-space>155584</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+ <Iteration_message>No hits found</Iteration_message>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>24</Iteration_iter-num>\n+ <Iteration_query-ID>Query_6</Iteration_query-ID>\n+ <Iteration_query-def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Iteration_query-def>\n+ <Iteration_query-len>1344</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>Subject_4</Hit_id>\n+ <Hit_def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Hit_def>\n+ <Hit_accession>Subject_4</Hit_accession>\n+ <Hit_len>348</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>532.717</Hsp_bit-score>\n+ <Hsp_score>1371</Hsp_score>\n+ <Hsp_evalue>0</Hsp_evalue>\n+ <Hsp_query-from>23</Hsp_query-from>\n+ <Hsp_query-to>1021</Hsp_query-to>\n+ <Hsp_hit-from>1</Hsp_hit-from>\n+ <Hsp_hit-to>333</Hsp_hit-to>\n+ <Hsp_query-frame>2</Hsp_query-frame>\n+ <Hsp_hit-frame>0</Hsp_hit-frame>\n+ <Hsp_identity>272</Hsp_identity>\n+ <Hsp_positive>307</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>333</Hsp_align-len>\n+ <Hsp_qseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKXXXXXXXXXXXXXXXXXXVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDG</Hsp_qseq>\n+ <Hsp_hseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEA</Hsp_hseq>\n+ <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE+HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA+YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR+CM+TT+CCGKNP +++ </Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>0</Statistics_db-num>\n+ <Statistics_db-len>0</Statistics_db-len>\n+ <Statistics_hsp-len>32</Statistics_hsp-len>\n+ <Statistics_eff-space>155584</Statistics_eff-space>\n+ <Statistics_kappa>0.041</Statistics_kappa>\n+ <Statistics_lambda>0.267</Statistics_lambda>\n+ <Statistics_entropy>0.14</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+</BlastOutput_iterations>\n+</BlastOutput>\n+\n' |
| b |
| diff -r b2795652d2b4 -r 5402f9b0d508 test-data/tblastn_four_human_vs_rhodopsin.html --- a/test-data/tblastn_four_human_vs_rhodopsin.html Mon Nov 25 10:58:46 2013 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.html Thu Nov 28 08:50:15 2013 -0500 |
| b |
| @@ -3,7 +3,7 @@ <BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099"> <PRE> -<b>TBLASTN 2.2.27+</b> +<b>TBLASTN 2.2.28+</b> <b>Query=</b> sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 |
| b |
| diff -r b2795652d2b4 -r 5402f9b0d508 test-data/tblastn_four_human_vs_rhodopsin.xml --- a/test-data/tblastn_four_human_vs_rhodopsin.xml Mon Nov 25 10:58:46 2013 -0500 +++ b/test-data/tblastn_four_human_vs_rhodopsin.xml Thu Nov 28 08:50:15 2013 -0500 |
| b |
| b'@@ -2,7 +2,7 @@\n <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n <BlastOutput>\n <BlastOutput_program>tblastn</BlastOutput_program>\n- <BlastOutput_version>TBLASTN 2.2.27+</BlastOutput_version>\n+ <BlastOutput_version>TBLASTN 2.2.28+</BlastOutput_version>\n <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&auml;ffer, 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.</BlastOutput_reference>\n <BlastOutput_db></BlastOutput_db>\n <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n@@ -17,706 +17,725 @@\n <Parameters_filter>F</Parameters_filter>\n </Parameters>\n </BlastOutput_param>\n- <BlastOutput_iterations>\n- <Iteration>\n- <Iteration_iter-num>1</Iteration_iter-num>\n- <Iteration_query-ID>Query_1</Iteration_query-ID>\n- <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>19</Statistics_hsp-len>\n- <Statistics_eff-space>127710</Statistics_eff-space>\n- <Statistics_kappa>0.071</Statistics_kappa>\n- <Statistics_lambda>0.299</Statistics_lambda>\n- <Statistics_entropy>0.27</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>2</Iteration_iter-num>\n- <Iteration_query-ID>Query_1</Iteration_query-ID>\n- <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>19</Statistics_hsp-len>\n- <Statistics_eff-space>127710</Statistics_eff-space>\n- <Statistics_kappa>0.071</Statistics_kappa>\n- <Statistics_lambda>0.299</Statistics_lambda>\n- <Statistics_entropy>0.27</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>3</Iteration_iter-num>\n- <Iteration_query-ID>Query_1</Iteration_query-ID>\n- <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iteration_hits></Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>0</Statistics_db-num>\n- <Statistics_db-len>0</Statistics_db-len>\n- <Statistics_hsp-len>19</Statistics_hsp-len>\n- <Statistics_eff-space>127710</Statistics_eff-space>\n- <Statistics_kappa>0.071</Statistics_kappa>\n- <Statistics_lambda>0.299</Statistics_lambda>\n- <Statistics_entropy>0.27</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n- </Iteration>\n- <Iteration>\n- <Iteration_iter-num>4</Iteration_iter-num>\n- <Iteration_query-ID>Query_1</Iteration_query-ID>\n- <Iteration_query-def>sp|Q9BS26|ERP44_HUMAN Endoplasmic reticulum resident protein 44 OS=Homo sapiens GN=ERP44 PE=1 SV=1</Iteration_query-def>\n- <Iteration_query-len>406</Iteration_query-len>\n- <Iter'..b'YYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA</Hsp_hseq>\n+ <Hsp_midline>MNGTEGPNFYVPFSN TGVVRSPFE PQYYLAEPWQFSMLAAYMFLLI+LGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMV GGFT+TLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPL GWSRYIPEG+QCSCGIDYYT E NNESFVIYMFVVHF IP+I+IFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICW+PYA VAFYIFTHQGS+FGPIFMTIPAFFAK++A+YNPVIYIMMNKQFRNCM+TT+CCGKNPLGDDEAS TVSKTETSQVAPA</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>0</Statistics_db-num>\n+ <Statistics_db-len>0</Statistics_db-len>\n+ <Statistics_hsp-len>18</Statistics_hsp-len>\n+ <Statistics_eff-space>109230</Statistics_eff-space>\n+ <Statistics_kappa>0.071</Statistics_kappa>\n+ <Statistics_lambda>0.299</Statistics_lambda>\n+ <Statistics_entropy>0.27</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>24</Iteration_iter-num>\n+ <Iteration_query-ID>Query_4</Iteration_query-ID>\n+ <Iteration_query-def>sp|P08100|OPSD_HUMAN Rhodopsin OS=Homo sapiens GN=RHO PE=1 SV=1</Iteration_query-def>\n+ <Iteration_query-len>348</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>Subject_6</Hit_id>\n+ <Hit_def>gi|12583664|dbj|AB043817.1| Conger myriaster conf gene for fresh water form rod opsin, complete cds</Hit_def>\n+ <Hit_accession>Subject_6</Hit_accession>\n+ <Hit_len>1344</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>626.708</Hsp_bit-score>\n+ <Hsp_score>1444</Hsp_score>\n+ <Hsp_evalue>0</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>341</Hsp_query-to>\n+ <Hsp_hit-from>23</Hsp_hit-from>\n+ <Hsp_hit-to>1048</Hsp_hit-to>\n+ <Hsp_query-frame>0</Hsp_query-frame>\n+ <Hsp_hit-frame>2</Hsp_hit-frame>\n+ <Hsp_identity>281</Hsp_identity>\n+ <Hsp_positive>311</Hsp_positive>\n+ <Hsp_gaps>1</Hsp_gaps>\n+ <Hsp_align-len>342</Hsp_align-len>\n+ <Hsp_qseq>MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVVHFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQGSNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPL-GDDEASATVSKTE</Hsp_qseq>\n+ <Hsp_hseq>MNGTEGPNFYIPMSNATGVVRSPFEYPQYYLAEPWAFSALSAYMFFLIIAGFPINFLTLYVTIEHKKLRTPLNYILLNLAVADLFMVFGGFTTTMYTSMHGYFVFGPTGCNIEGFFATLGGEIALWCLVVLAIERWMVVCKPVTNFRFGESHAIMGVMVTWTMALACALPPLFGWSRYIPEGLQCSCGIDYYTRAPGINNESFVIYMFTCHFSIPLAVISFCYGRLVCTVKEAAAQQQESETTQRAEREVTRMVVIMVISFLVCWVPYASVAWYIFTHQGSTFGPIFMTIPSFFAKSSALYNPMIYICMNKQFRHCMITTLCCGKNPFEEEDGASATSSKTE</Hsp_hseq>\n+ <Hsp_midline>MNGTEGPNFY+P SNATGVVRSPFEYPQYYLAEPW FS L+AYMF LI+ GFPINFLTLYVT++HKKLRTPLNYILLNLAVADLFMV GGFT+T+YTS+HGYFVFGPTGCN+EGFFATLGGEIALW LVVLAIER++VVCKP++NFRFGE HAIMGV TW MALACA PPL GWSRYIPEGLQCSCGIDYYT P +NNESFVIYMF HF+IP+ +I FCYG+LV TVKEAAAQQQES TTQ+AE+EVTRMV+IMVI+FL+CWVPYASVA YIFTHQGS FGPIFMTIP+FFAKS+A+YNP+IYI MNKQFR CM+TT+CCGKNP +D ASAT SKTE</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>0</Statistics_db-num>\n+ <Statistics_db-len>0</Statistics_db-len>\n+ <Statistics_hsp-len>18</Statistics_hsp-len>\n+ <Statistics_eff-space>109230</Statistics_eff-space>\n+ <Statistics_kappa>0.071</Statistics_kappa>\n+ <Statistics_lambda>0.299</Statistics_lambda>\n+ <Statistics_entropy>0.27</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+</BlastOutput_iterations>\n+</BlastOutput>\n+\n' |
| b |
| diff -r b2795652d2b4 -r 5402f9b0d508 tools/ncbi_blast_plus/README.rst --- a/tools/ncbi_blast_plus/README.rst Mon Nov 25 10:58:46 2013 -0500 +++ b/tools/ncbi_blast_plus/README.rst Thu Nov 28 08:50:15 2013 -0500 |
| b |
| @@ -5,7 +5,7 @@ (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved. See the licence text below. -Currently tested with NCBI BLAST 2.2.27+ (i.e. version 2.2.27 of BLAST+), +Currently tested with NCBI BLAST 2.2.28+ (i.e. version 2.2.28 of BLAST+), and does not work with the NCBI 'legacy' BLAST suite (e.g. blastall). Note that these wrappers (and the associated datatypes) were originally @@ -71,7 +71,7 @@ about any system level BLAST databases using the tool-data/blastdb*.loc files. You must install the NCBI BLAST+ standalone tools somewhere on the system -path. Currently the unit tests are written using "BLAST 2.2.27+". +path. Currently the unit tests are written using "BLAST 2.2.28+". Run the functional tests (adjusting the section identifier to match your tool_conf.xml.sample file):: @@ -131,6 +131,9 @@ - Set number of threads via $GALAXY_SLOTS environment variable - More descriptive default output names - Tests require updated BLAST DB definitions (blast_datatypes v0.0.18) + - Pre-check for duplicate identifiers in makeblastdb wrapper. + - Tests updated for BLAST+ 2.2.28 instead of BLAST+ 2.2.27 + - Now depends on package_blast_plus_2_2_28 in ToolShed ======= ====================================================================== |
| b |
| diff -r b2795652d2b4 -r 5402f9b0d508 tools/ncbi_blast_plus/check_no_duplicates.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/ncbi_blast_plus/check_no_duplicates.py Thu Nov 28 08:50:15 2013 -0500 |
| [ |
| @@ -0,0 +1,46 @@ +#!/usr/bin/env python +"""Check for duplicate sequence identifiers in FASTA files. + +This is run as a pre-check before makeblastdb, in order to avoid +a regression bug in BLAST+ 2.2.28 which fails to catch this. See: +http://blastedbio.blogspot.co.uk/2012/10/my-ids-not-good-enough-for-ncbi-blast.html + +This script takes one or more FASTA filenames as input, and +will return a non-zero error if any duplicate identifiers +are found. +""" +import sys +import os + +if "-v" in sys.argv or "--version" in sys.argv: + print("v0.0.22") + sys.exit(0) + +def stop_err(msg, error=1): + sys.stderr.write("%s\n" % msg) + sys.exit(error) + + +identifiers = set() +files = 0 +for filename in sys.argv[1:]: + if not os.path.isfile(filename): + stop_err("Missing FASTA file %r" % filename, 2) + files += 1 + handle = open(filename) + for line in handle: + if line.startswith(">"): + #The split will also take care of the new line character, + #e.g. ">test\n" and ">test description here\n" both give "test" + seq_id = line[1:].split(None, 1)[0] + if seq_id in identifiers: + handle.close() + stop_err("Repeated identifiers, e.g. %r" % seq_id, 1) + identifiers.add(seq_id) + handle.close() +if not files: + stop_err("No FASTA files given to check for duplicates", 3) +elif files == 1: + print("%i sequences" % len(identifiers)) +else: + print("%i sequences in %i FASTA files" % (len(identifiers), files)) |
| b |
| diff -r b2795652d2b4 -r 5402f9b0d508 tools/ncbi_blast_plus/ncbi_macros.xml --- a/tools/ncbi_blast_plus/ncbi_macros.xml Mon Nov 25 10:58:46 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_macros.xml Thu Nov 28 08:50:15 2013 -0500 |
| b |
| @@ -240,7 +240,7 @@ <xml name="requirements"> <requirements> <requirement type="binary">@BINARY@</requirement> - <requirement type="package" version="2.2.27">blast+</requirement> + <requirement type="package" version="2.2.28">blast+</requirement> </requirements> <version_command>@BINARY@ -version</version_command> </xml> |
| b |
| diff -r b2795652d2b4 -r 5402f9b0d508 tools/ncbi_blast_plus/ncbi_makeblastdb.xml --- a/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Nov 25 10:58:46 2013 -0500 +++ b/tools/ncbi_blast_plus/ncbi_makeblastdb.xml Thu Nov 28 08:50:15 2013 -0500 |
| b |
| @@ -5,7 +5,13 @@ <import>ncbi_macros.xml</import> </macros> <expand macro="requirements" /> - <command> + <command interpreter="python">check_no_duplicates.py +##First check for duplicates (since BLAST+ 2.2.28 fails to do so) +##and abort (via the ampersand ampersand trick) if any are found. +#for $i in $in +"${i.file}" +#end for +&& makeblastdb -out "${os.path.join($outfile.extra_files_path,'blastdb')}" $parse_seqids $hash_index |