| Previous changeset 31:344cd76f6fd2 (2014-05-15) Next changeset 33:3bb5da68305e (2014-05-15) |
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Commit message:
fix tests |
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modified:
tool_dependencies.xml |
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added:
test-data/blast xml example1.html test-data/blast xml example2.html test-data/blast xml example3.html test-data/blast xml example3.xml test-data/blast xml example4.html test-data/blast xml example4.xml |
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removed:
test-data/Galaxy19-[blastn_EUginius_primers_probes.fasta_vs_EUginius_plasmid_insert.fasta_].blastxml test-data/Galaxy8-[blastn-short_EUginius_primers_probes.fasta_vs__EUginius_].blastxml |
| [ |
| diff -r 344cd76f6fd2 -r ce8f29efc0a1 test-data/Galaxy19-[blastn_EUginius_primers_probes.fasta_vs_EUginius_plasmid_insert.fasta_].blastxml --- a/test-data/Galaxy19-[blastn_EUginius_primers_probes.fasta_vs_EUginius_plasmid_insert.fasta_].blastxml Thu May 15 16:59:18 2014 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1387 +0,0 @@\n-<?xml version="1.0"?>\n-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n-<BlastOutput>\n- <BlastOutput_program>blastn</BlastOutput_program>\n- <BlastOutput_version>BLASTN 2.2.29+</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- <BlastOutput_query-def>Forward_Primer|NOST-Spec_(Genetic_ID)</BlastOutput_query-def>\n- <BlastOutput_query-len>20</BlastOutput_query-len>\n- <BlastOutput_param>\n- <Parameters>\n- <Parameters_expect>0.001</Parameters_expect>\n- <Parameters_sc-match>2</Parameters_sc-match>\n- <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>\n- <Parameters_gap-open>5</Parameters_gap-open>\n- <Parameters_gap-extend>2</Parameters_gap-extend>\n- <Parameters_filter>L;m;</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>\n- <Iteration_query-len>20</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>8</Statistics_hsp-len>\n- <Statistics_eff-space>12312</Statistics_eff-space>\n- <Statistics_kappa>0.41</Statistics_kappa>\n- <Statistics_lambda>0.625</Statistics_lambda>\n- <Statistics_entropy>0.78</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>\n- <Iteration_query-len>20</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>8</Statistics_hsp-len>\n- <Statistics_eff-space>12312</Statistics_eff-space>\n- <Statistics_kappa>0.41</Statistics_kappa>\n- <Statistics_lambda>0.625</Statistics_lambda>\n- <Statistics_entropy>0.78</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>\n- <Iteration_query-len>20</Iteration_query-len>\n-<Iteration_hits>\n-<Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>Subject_3</Hit_id>\n- <Hit_def>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</Hit_def>\n- <Hit_accession>Subject_3</Hit_accession>\n- <Hit_len>323</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>37.3537</Hsp_bit-score>\n- <Hsp_score>40</Hsp_score>\n- <Hsp_evalue>7.01052e-08</Hsp_evalue>\n- <Hsp_query-from>1</Hsp_query-from>\n- <Hsp_query-to>20</Hsp_query-to>\n- <Hsp_hit-from>200</Hsp_hit-from>\n- <Hsp_hit-to>219</Hsp_hit-to>\n- <Hsp_query-frame>1</Hsp_query-frame>\n- <Hsp_hit-frame>1</Hsp_hit-frame>\n- <Hsp_identity>20</Hsp_identity>\n- <Hsp_positive>20</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>20</Hsp_align-len>\n- <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq>\n- <Hsp_hseq>AGCGCGCAAACTAGGAT'..b'bda>\n- <Statistics_entropy>0.78</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n- <Iteration_message>No hits found</Iteration_message>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>55</Iteration_iter-num>\n- <Iteration_query-ID>Query_7</Iteration_query-ID>\n- <Iteration_query-def>Amplicon|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>\n- <Iteration_query-len>74</Iteration_query-len>\n-<Iteration_hits>\n-<Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>Subject_7</Hit_id>\n- <Hit_def>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</Hit_def>\n- <Hit_accession>Subject_7</Hit_accession>\n- <Hit_len>4180</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>89.6514</Hsp_bit-score>\n- <Hsp_score>98</Hsp_score>\n- <Hsp_evalue>6.62923e-23</Hsp_evalue>\n- <Hsp_query-from>1</Hsp_query-from>\n- <Hsp_query-to>74</Hsp_query-to>\n- <Hsp_hit-from>1516</Hsp_hit-from>\n- <Hsp_hit-to>1589</Hsp_hit-to>\n- <Hsp_query-frame>1</Hsp_query-frame>\n- <Hsp_hit-frame>1</Hsp_hit-frame>\n- <Hsp_identity>64</Hsp_identity>\n- <Hsp_positive>64</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>74</Hsp_align-len>\n- <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>\n- <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>\n- <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</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>11</Statistics_hsp-len>\n- <Statistics_eff-space>64449</Statistics_eff-space>\n- <Statistics_kappa>0.41</Statistics_kappa>\n- <Statistics_lambda>0.625</Statistics_lambda>\n- <Statistics_entropy>0.78</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>56</Iteration_iter-num>\n- <Iteration_query-ID>Query_7</Iteration_query-ID>\n- <Iteration_query-def>Amplicon|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>\n- <Iteration_query-len>74</Iteration_query-len>\n-<Iteration_hits>\n-<Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>Subject_8</Hit_id>\n- <Hit_def>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</Hit_def>\n- <Hit_accession>Subject_8</Hit_accession>\n- <Hit_len>4983</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>89.6514</Hsp_bit-score>\n- <Hsp_score>98</Hsp_score>\n- <Hsp_evalue>6.62923e-23</Hsp_evalue>\n- <Hsp_query-from>1</Hsp_query-from>\n- <Hsp_query-to>74</Hsp_query-to>\n- <Hsp_hit-from>2319</Hsp_hit-from>\n- <Hsp_hit-to>2392</Hsp_hit-to>\n- <Hsp_query-frame>1</Hsp_query-frame>\n- <Hsp_hit-frame>1</Hsp_hit-frame>\n- <Hsp_identity>64</Hsp_identity>\n- <Hsp_positive>64</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>74</Hsp_align-len>\n- <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>\n- <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>\n- <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</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>11</Statistics_hsp-len>\n- <Statistics_eff-space>64449</Statistics_eff-space>\n- <Statistics_kappa>0.41</Statistics_kappa>\n- <Statistics_lambda>0.625</Statistics_lambda>\n- <Statistics_entropy>0.78</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n-</Iteration>\n-</BlastOutput_iterations>\n-</BlastOutput>\n-\n' |
| [ |
| diff -r 344cd76f6fd2 -r ce8f29efc0a1 test-data/Galaxy8-[blastn-short_EUginius_primers_probes.fasta_vs__EUginius_].blastxml --- a/test-data/Galaxy8-[blastn-short_EUginius_primers_probes.fasta_vs__EUginius_].blastxml Thu May 15 16:59:18 2014 +0200 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,412 +0,0 @@\n-<?xml version="1.0"?>\n-<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n-<BlastOutput>\n- <BlastOutput_program>blastn</BlastOutput_program>\n- <BlastOutput_version>BLASTN 2.2.29+</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>/opt/galaxy/blastdbs/EUginius_plasmid_insert</BlastOutput_db>\n- <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n- <BlastOutput_query-def>Forward_Primer|NOST-Spec_(Genetic_ID)</BlastOutput_query-def>\n- <BlastOutput_query-len>20</BlastOutput_query-len>\n- <BlastOutput_param>\n- <Parameters>\n- <Parameters_expect>0.001</Parameters_expect>\n- <Parameters_sc-match>1</Parameters_sc-match>\n- <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>\n- <Parameters_gap-open>5</Parameters_gap-open>\n- <Parameters_gap-extend>2</Parameters_gap-extend>\n- <Parameters_filter>L;m;</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>\n- <Iteration_query-len>20</Iteration_query-len>\n-<Iteration_hits>\n-<Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>gnl|BL_ORD_ID|5</Hit_id>\n- <Hit_def>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</Hit_def>\n- <Hit_accession>5</Hit_accession>\n- <Hit_len>2457</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>40.14</Hsp_bit-score>\n- <Hsp_score>20</Hsp_score>\n- <Hsp_evalue>1.51296e-07</Hsp_evalue>\n- <Hsp_query-from>1</Hsp_query-from>\n- <Hsp_query-to>20</Hsp_query-to>\n- <Hsp_hit-from>2119</Hsp_hit-from>\n- <Hsp_hit-to>2138</Hsp_hit-to>\n- <Hsp_query-frame>1</Hsp_query-frame>\n- <Hsp_hit-frame>1</Hsp_hit-frame>\n- <Hsp_identity>20</Hsp_identity>\n- <Hsp_positive>20</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>20</Hsp_align-len>\n- <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq>\n- <Hsp_hseq>AGCGCGCAAACTAGGATAAA</Hsp_hseq>\n- <Hsp_midline>||||||||||||||||||||</Hsp_midline>\n- </Hsp>\n- </Hit_hsps>\n-</Hit>\n-<Hit>\n- <Hit_num>2</Hit_num>\n- <Hit_id>gnl|BL_ORD_ID|2</Hit_id>\n- <Hit_def>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</Hit_def>\n- <Hit_accession>2</Hit_accession>\n- <Hit_len>323</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>40.14</Hsp_bit-score>\n- <Hsp_score>20</Hsp_score>\n- <Hsp_evalue>1.51296e-07</Hsp_evalue>\n- <Hsp_query-from>1</Hsp_query-from>\n- <Hsp_query-to>20</Hsp_query-to>\n- <Hsp_hit-from>200</Hsp_hit-from>\n- <Hsp_hit-to>219</Hsp_hit-to>\n- <Hsp_query-frame>1</Hsp_query-frame>\n- <Hsp_hit-frame>1</Hsp_hit-frame>\n- <Hsp_identity>20</Hsp_identity>\n- <Hsp_positive>20</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>20</Hsp_align-len>\n- <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq>\n- <Hsp_hseq>AGCGCGCAAACTAGGATAAA</Hsp_hseq>\n- <Hsp_midline>||||||||||||||||||||</Hsp_midline>\n- </Hsp>\n- </Hit_hsps>\n-</Hit>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>8</Statistics_db-num>\n- <Statistics_db-len>15339</Statistics_db-len>\n- <Statistics_hsp-len>8</Statistics_hsp-len>\n- <Statistics_eff-space>183300</Statistics_eff-space>\n- <Statistics_kappa>0.710602795216363</Statistics_kappa>\n- <Statistics_la'..b'rame>\n- <Hsp_identity>21</Hsp_identity>\n- <Hsp_positive>21</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>22</Hsp_align-len>\n- <Hsp_qseq>ACATGAACAGCGCCTTGACCAC</Hsp_qseq>\n- <Hsp_hseq>ACATGAACAGCGCCCTGACCAC</Hsp_hseq>\n- <Hsp_midline>|||||||||||||| |||||||</Hsp_midline>\n- </Hsp>\n- </Hit_hsps>\n-</Hit>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>8</Statistics_db-num>\n- <Statistics_db-len>15339</Statistics_db-len>\n- <Statistics_hsp-len>9</Statistics_hsp-len>\n- <Statistics_eff-space>244272</Statistics_eff-space>\n- <Statistics_kappa>0.710602795216363</Statistics_kappa>\n- <Statistics_lambda>1.37406312246009</Statistics_lambda>\n- <Statistics_entropy>1.30724660390929</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n-</Iteration>\n-<Iteration>\n- <Iteration_iter-num>7</Iteration_iter-num>\n- <Iteration_query-ID>Query_7</Iteration_query-ID>\n- <Iteration_query-def>Amplicon|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>\n- <Iteration_query-len>74</Iteration_query-len>\n-<Iteration_hits>\n-<Hit>\n- <Hit_num>1</Hit_num>\n- <Hit_id>gnl|BL_ORD_ID|7</Hit_id>\n- <Hit_def>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</Hit_def>\n- <Hit_accession>7</Hit_accession>\n- <Hit_len>4983</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>67.8929</Hsp_bit-score>\n- <Hsp_score>34</Hsp_score>\n- <Hsp_evalue>3.56369e-15</Hsp_evalue>\n- <Hsp_query-from>1</Hsp_query-from>\n- <Hsp_query-to>74</Hsp_query-to>\n- <Hsp_hit-from>2319</Hsp_hit-from>\n- <Hsp_hit-to>2392</Hsp_hit-to>\n- <Hsp_query-frame>1</Hsp_query-frame>\n- <Hsp_hit-frame>1</Hsp_hit-frame>\n- <Hsp_identity>64</Hsp_identity>\n- <Hsp_positive>64</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>74</Hsp_align-len>\n- <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>\n- <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>\n- <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</Hsp_midline>\n- </Hsp>\n- </Hit_hsps>\n-</Hit>\n-<Hit>\n- <Hit_num>2</Hit_num>\n- <Hit_id>gnl|BL_ORD_ID|6</Hit_id>\n- <Hit_def>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</Hit_def>\n- <Hit_accession>6</Hit_accession>\n- <Hit_len>4180</Hit_len>\n- <Hit_hsps>\n- <Hsp>\n- <Hsp_num>1</Hsp_num>\n- <Hsp_bit-score>67.8929</Hsp_bit-score>\n- <Hsp_score>34</Hsp_score>\n- <Hsp_evalue>3.56369e-15</Hsp_evalue>\n- <Hsp_query-from>1</Hsp_query-from>\n- <Hsp_query-to>74</Hsp_query-to>\n- <Hsp_hit-from>1516</Hsp_hit-from>\n- <Hsp_hit-to>1589</Hsp_hit-to>\n- <Hsp_query-frame>1</Hsp_query-frame>\n- <Hsp_hit-frame>1</Hsp_hit-frame>\n- <Hsp_identity>64</Hsp_identity>\n- <Hsp_positive>64</Hsp_positive>\n- <Hsp_gaps>0</Hsp_gaps>\n- <Hsp_align-len>74</Hsp_align-len>\n- <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>\n- <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>\n- <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</Hsp_midline>\n- </Hsp>\n- </Hit_hsps>\n-</Hit>\n-</Iteration_hits>\n- <Iteration_stat>\n- <Statistics>\n- <Statistics_db-num>8</Statistics_db-num>\n- <Statistics_db-len>15339</Statistics_db-len>\n- <Statistics_hsp-len>10</Statistics_hsp-len>\n- <Statistics_eff-space>976576</Statistics_eff-space>\n- <Statistics_kappa>0.710602795216363</Statistics_kappa>\n- <Statistics_lambda>1.37406312246009</Statistics_lambda>\n- <Statistics_entropy>1.30724660390929</Statistics_entropy>\n- </Statistics>\n- </Iteration_stat>\n-</Iteration>\n-</BlastOutput_iterations>\n-</BlastOutput>\n-\n' |
| b |
| diff -r 344cd76f6fd2 -r ce8f29efc0a1 test-data/blast xml example1.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example1.html Thu May 15 17:22:02 2014 +0200 |
| b |
| b'@@ -0,0 +1,13220 @@\n+<!DOCTYPE html>\n+<html>\n+ <head>\n+ <meta charset="UTF-8">\n+ <meta name=generator content="blast2html; see ...">\n+ \n+ <title>Blast output</title>\n+ \n+ <style>\n+ body {\n+ color: #333333;\n+ font-family: Arial,Sans-Serif;\n+ }\n+\n+ :link {\n+ color: #336699;\n+ }\n+\n+ .right {\n+ float: right;\n+ }\n+\n+ /* Galaxy with html sanitization enabled strips the header of this html page. If so, show the user a warning.*/\n+ #strip_html_warning {\n+ display: none;\n+ }\n+ \n+ #content {\n+ margin: 0 2em;\n+ padding: 0.5em;\n+ border: 1px solid #888888;\n+ background-color: #d3dff5;\n+ }\n+\n+ h1, h2, h3, h4, h5, h6 {\n+ color: #2A6979;\n+ font-family: arial,verdana,sans-serif;\n+ letter-spacing: -1px;\n+ margin: 1.2em 0 0.3em;\n+ }\n+\n+ h1 {\n+ border-bottom: 1px solid #CCCCCC;\n+ font-size: 150%;\n+ padding-bottom: 0.1em;\n+ }\n+\n+ h2 {\n+ font-size: 120%;\n+ font-weight: bold;\n+ }\n+\n+ h4.darkHeader {\n+ color: #4D4D4D;\n+ letter-spacing: 0;\n+ font-weight: bold;\n+ }\n+\n+ #nodata {\n+ font-weight: bold;\n+ }\n+\n+ .index {\n+ margin-bottom: 3em;\n+ }\n+ .index div.indexentry {\n+ margin: 1.2em 1.6em;\n+ font-weight: bold;\n+ font-size: 100%;\n+ }\n+ \n+ .headerdata {\n+ font-size: 90%;\n+ }\n+ .headerdata .param {\n+ font-weight: bold;\n+ text-align: right;\n+ padding: 0 1em;\n+ }\n+\n+ .grey {\n+ background-color: #eeeeee;\n+ border: 1px solid #cccccc;\n+ padding: 1em;\n+ }\n+\n+ .white {\n+ background-color: white;\n+ border: 1px solid #cccccc;\n+ padding: 1.5em 2%;\n+ }\n+\n+ .graphicrow {\n+ clear: left;\n+ width: 100%;\n+ }\n+\n+ .graphicitem {\n+ float: left;\n+ }\n+\n+\n+ \n+ .graphics .grey {\n+ text-align: center;\n+ }\n+\n+ .graphic {\n+ background-color: white;\n+ border: 2px solid black;\n+ padding: 1.5em;\n+ margin: auto;\n+ }\n+\n+ .centered, .defline, div.legend, div.tablewrapper {\n+ margin-left: auto;\n+ margin-right: auto;\n+ }\n+\n+ .defline {\n+ background-color: white;\n+ border: 1px solid black;\n+ margin: .5em auto;\n+ padding-left: .2em;\n+ padding-right: .2em;\n+ max-width: 50em;\n+ text-align: left;\n+ height: 2.8em;\n+ overflow-y: hidden;\n+ }\n+\n+ div.legend {\n+ max-width: 40em;\n+ }\n+ div.legend div {\n+ width: 100%;\n+ color: white;\n+ font-weight: bold;\n+ border-spacing: 0;\n+ }\n+ div.legend div .graphicitem {\n+ width: 20%;\n+ padding: 0;\n+ margin: 0;\n+ border: none;\n+ }\n+\n+ div.tablewrapper {\n+ width: 50%;\n+ min-width: 60em;\n+ }\n+\n+ /* For small widths we give the graphic 100% */\n+ @media (max-width: 72.5em) {\n+ div.tablewrapper {\n+ width: 100%;\n+ min-width: 0px;\n+ }\n+ }\n+\n+ .scale {\n+ width: 100%;\n+ margin: .5em 0;\n+ font-weight: bold;\n+ }\n+ .scale div {\n+ color: red;\n+ text-align: left;\n+ }\n+ .scale .graphicrow {\n+ margin: .5em 0 .5em 0;\n+ color: white;\n+ }\n+ .scale .graphicitem {\n+ position: relative;\n+ }\n+ .scale .graphicitem div {\n+ margin: 0 1px;\n+ padding: 0 2px;\n+ text-align: right;\n+ background-color: red;\n+ color: white;\n+ }\n+ .scale .graphicitem:first-child div {\n+ margin-left: 0px;\n+ }\n+ .scale .graphicitem:last-child div {\n+ margin-right: 0px;\n+ }\n+ .scale .graphicitem .lastlabel {\n+ position: absolute;\n+ top: 0px;\n+ left: 100%;\n+ background-color: transparent;\n+ color: red;\n+ }\n+\n+ a.matchresult {\n+ display: block;\n+ margin: 0;\n+ padding'..b'on Plus 2 (In The B Strand) In The Presence Of Magnesium</p>\n+ <p class=titleinfo>\n+ <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/393715375?report=genbank&log$=nuclalign">pdb|4AQX|C</a>\n+ <span class=b>Length:</span> 14\n+ <span class=b>Number of Matches:</span> 1\n+ </p>\n+ </div>\n+\n+\n+ <div class=hotspot>\n+ <p class=range>\n+ <span class=range>Range 1: 7 to 14</span>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/393715375?report=genbank&log$=nuclalign&from=7&to=14">GenBank</a>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/393715375?report=graph&log$=nuclalign&from=7&to=14">Graphics</a>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>16.4 bits(8)</td>\n+ <td>47.0</td>\n+ <td>8/8(100%)</td>\n+ <td>0/8(0%)</td>\n+ <td>Plus/Plus</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>Query 5 CGTCGTGA 12\n+ ||||||||\n+Subject 7 CGTCGTGA 14</pre>\n+ </div>\n+\n+ </div>\n+\n+ <div class=alignment id=hit100>\n+\n+ <div class=linkheader>\n+ <div class=right><a href="#description100">Descriptions</a></div>\n+ <a class=linkheader href="http://www.ncbi.nlm.nih.gov/nucleotide/393715371?report=genbank&log$=nuclalign">GenBank</a>\n+ <a class=linkheader href="http://www.ncbi.nlm.nih.gov/nucleotide/393715371?report=graph&log$=nuclalign">Graphics</a>\n+ </div>\n+\n+ <div class=title>\n+ <p class=hittitle>Chain C, Crystal Structure Of I-Crei Complexed With Its Target Methylated At Position Plus 2 (In The B Strand) In The Presence Of Calcium</p>\n+ <p class=titleinfo>\n+ <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/393715371?report=genbank&log$=nuclalign">pdb|4AQU|C</a>\n+ <span class=b>Length:</span> 24\n+ <span class=b>Number of Matches:</span> 1\n+ </p>\n+ </div>\n+\n+\n+ <div class=hotspot>\n+ <p class=range>\n+ <span class=range>Range 1: 7 to 14</span>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/393715371?report=genbank&log$=nuclalign&from=7&to=14">GenBank</a>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/393715371?report=graph&log$=nuclalign&from=7&to=14">Graphics</a>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>16.4 bits(8)</td>\n+ <td>47.0</td>\n+ <td>8/8(100%)</td>\n+ <td>0/8(0%)</td>\n+ <td>Plus/Plus</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>Query 5 CGTCGTGA 12\n+ ||||||||\n+Subject 7 CGTCGTGA 14</pre>\n+ </div>\n+\n+ </div>\n+\n+ </div></div>\n+ </section>\n+ </section>\n+\n+ </div>\n+\n+ <footer>\n+ This page was generated by <a href="...">blast2html</a>.\n+ </footer>\n+ </body>\n+</html>\n+\n' |
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| diff -r 344cd76f6fd2 -r ce8f29efc0a1 test-data/blast xml example2.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example2.html Thu May 15 17:22:02 2014 +0200 |
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| b'@@ -0,0 +1,424 @@\n+<!DOCTYPE html>\n+<html>\n+ <head>\n+ <meta charset="UTF-8">\n+ <meta name=generator content="blast2html; see ...">\n+ \n+ <title>Blast output</title>\n+ \n+ <style>\n+ body {\n+ color: #333333;\n+ font-family: Arial,Sans-Serif;\n+ }\n+\n+ :link {\n+ color: #336699;\n+ }\n+\n+ .right {\n+ float: right;\n+ }\n+\n+ /* Galaxy with html sanitization enabled strips the header of this html page. If so, show the user a warning.*/\n+ #strip_html_warning {\n+ display: none;\n+ }\n+ \n+ #content {\n+ margin: 0 2em;\n+ padding: 0.5em;\n+ border: 1px solid #888888;\n+ background-color: #d3dff5;\n+ }\n+\n+ h1, h2, h3, h4, h5, h6 {\n+ color: #2A6979;\n+ font-family: arial,verdana,sans-serif;\n+ letter-spacing: -1px;\n+ margin: 1.2em 0 0.3em;\n+ }\n+\n+ h1 {\n+ border-bottom: 1px solid #CCCCCC;\n+ font-size: 150%;\n+ padding-bottom: 0.1em;\n+ }\n+\n+ h2 {\n+ font-size: 120%;\n+ font-weight: bold;\n+ }\n+\n+ h4.darkHeader {\n+ color: #4D4D4D;\n+ letter-spacing: 0;\n+ font-weight: bold;\n+ }\n+\n+ #nodata {\n+ font-weight: bold;\n+ }\n+\n+ .index {\n+ margin-bottom: 3em;\n+ }\n+ .index div.indexentry {\n+ margin: 1.2em 1.6em;\n+ font-weight: bold;\n+ font-size: 100%;\n+ }\n+ \n+ .headerdata {\n+ font-size: 90%;\n+ }\n+ .headerdata .param {\n+ font-weight: bold;\n+ text-align: right;\n+ padding: 0 1em;\n+ }\n+\n+ .grey {\n+ background-color: #eeeeee;\n+ border: 1px solid #cccccc;\n+ padding: 1em;\n+ }\n+\n+ .white {\n+ background-color: white;\n+ border: 1px solid #cccccc;\n+ padding: 1.5em 2%;\n+ }\n+\n+ .graphicrow {\n+ clear: left;\n+ width: 100%;\n+ }\n+\n+ .graphicitem {\n+ float: left;\n+ }\n+\n+\n+ \n+ .graphics .grey {\n+ text-align: center;\n+ }\n+\n+ .graphic {\n+ background-color: white;\n+ border: 2px solid black;\n+ padding: 1.5em;\n+ margin: auto;\n+ }\n+\n+ .centered, .defline, div.legend, div.tablewrapper {\n+ margin-left: auto;\n+ margin-right: auto;\n+ }\n+\n+ .defline {\n+ background-color: white;\n+ border: 1px solid black;\n+ margin: .5em auto;\n+ padding-left: .2em;\n+ padding-right: .2em;\n+ max-width: 50em;\n+ text-align: left;\n+ height: 2.8em;\n+ overflow-y: hidden;\n+ }\n+\n+ div.legend {\n+ max-width: 40em;\n+ }\n+ div.legend div {\n+ width: 100%;\n+ color: white;\n+ font-weight: bold;\n+ border-spacing: 0;\n+ }\n+ div.legend div .graphicitem {\n+ width: 20%;\n+ padding: 0;\n+ margin: 0;\n+ border: none;\n+ }\n+\n+ div.tablewrapper {\n+ width: 50%;\n+ min-width: 60em;\n+ }\n+\n+ /* For small widths we give the graphic 100% */\n+ @media (max-width: 72.5em) {\n+ div.tablewrapper {\n+ width: 100%;\n+ min-width: 0px;\n+ }\n+ }\n+\n+ .scale {\n+ width: 100%;\n+ margin: .5em 0;\n+ font-weight: bold;\n+ }\n+ .scale div {\n+ color: red;\n+ text-align: left;\n+ }\n+ .scale .graphicrow {\n+ margin: .5em 0 .5em 0;\n+ color: white;\n+ }\n+ .scale .graphicitem {\n+ position: relative;\n+ }\n+ .scale .graphicitem div {\n+ margin: 0 1px;\n+ padding: 0 2px;\n+ text-align: right;\n+ background-color: red;\n+ color: white;\n+ }\n+ .scale .graphicitem:first-child div {\n+ margin-left: 0px;\n+ }\n+ .scale .graphicitem:last-child div {\n+ margin-right: 0px;\n+ }\n+ .scale .graphicitem .lastlabel {\n+ position: absolute;\n+ top: 0px;\n+ left: 100%;\n+ background-color: transparent;\n+ color: red;\n+ }\n+\n+ a.matchresult {\n+ display: block;\n+ margin: 0;\n+ padding: '..b'r {\n+ margin-right: 1em;\n+ }\n+ div.linkheader .right a {\n+ text-decoration: none;\n+ }\n+\n+ .title .hittitle {\n+ color: #222222;\n+ margin-bottom: .3em;\n+ }\n+ .title .titleinfo {\n+ font-size: 80%;\n+ margin-top: 0;\n+ margin-bottom: .3em;\n+ }\n+ .title .titleinfo .b {\n+ color: #606060;\n+ font-weight: bold;\n+ font-size: 90%;\n+ }\n+\n+ .moretitles {\n+ margin: 1.2em;\n+ }\n+ .moretitles .titleinfo {\n+ margin: 0;\n+ padding: 0;\n+ }\n+ .moretitles .hittitle {\n+ margin: .4em 0 .2em 0;\n+ padding: 0;\n+ }\n+ \n+ a.showmoretitles {\n+ font-size: 75%;\n+ color: #336699;\n+ font-weight: bold;\n+ margin-top: 0;\n+ }\n+ a.showmoretitles:hover {\n+ }\n+\n+ .hotspot {\n+ color: #606060;\n+ font-family: verdana, arial, sans-serif;\n+ margin-bottom: 2.5em;\n+ }\n+\n+ .hotspot p.range {\n+ font-size: 70%;\n+ margin-top: 0;\n+ margin-top: 1em;\n+ margin-bottom: .2em;\n+ }\n+ .hotspot p.range span.range {\n+ font-weight: bold;\n+ }\n+ .hotspot p.range a.range {\n+ margin-left: .5em;\n+ }\n+\n+ table.hotspotstable {\n+ border-top: 1px solid;\n+ border-bottom: 1px solid;\n+ text-align: left;\n+ border-collapse: collapse;\n+ }\n+ table.hotspotstable th, table.hotspotstable td {\n+ padding: .1em 1em;\n+ }\n+ table.hotspotstable th {\n+ font-size: 70%;\n+ }\n+ table.hotspotstable td {\n+ min-width: 7em;\n+ color: #222222;\n+ font-size: 80%;\n+ }\n+\n+ pre.alignmentgraphic {\n+ color: #222222;\n+ }\n+\n+ footer {\n+ text-align: center;\n+ color: #cccccc;\n+ font-size: 70%;\n+ margin-top: 1em;\n+ }\n+ footer :link {\n+ color: #5588cc;\n+ }\n+ \n+ </style>\n+\n+ <script type="text/javascript">\n+ function toggle_visibility(id) {\n+ var e = document.getElementById(id);\n+ if(e.style.display != \'block\')\n+ e.style.display = \'block\';\n+ else\n+ e.style.display = \'none\';\n+ }\n+ </script>\n+\n+ </head>\n+\n+ \n+ <body>\n+ \n+ <div id="strip_html_warning">\n+ <!-- This div should be hidden by the header css block. Galaxy\n+ strips all css, breaking this page but making this warning\n+ visible. This warning contains some ugly old skool tabular html\n+ layout that is not stripped. -->\n+ <table bgcolor="#FFE5C9"><tr><td><font color="red"><b>\n+ <font size=5><center>This html page seems to have been stripped by Galaxy.</center></font>\n+ Disable Galaxy\'s html sanitization feature to view the full page (see <font face=monospace>sanitize_all_html</font> in your galaxy\'s universe_wsgi.ini), or download this page instead of viewing it in Galaxy.\n+ </b></font></td></tr></table>\n+ </div>\n+ \n+ <div id=content>\n+\n+\n+\n+ \n+ <section class=match id=match1>\n+ \n+ <h1>Nucleotide Sequence (16 letters)</h1>\n+\n+ <section class=header>\n+\n+ <table class=headerdata>\n+ <tr><td class=param>Query ID:</td><td>Query_1</td></tr>\n+ <tr><td class=param>Query definition:</td><td>No definition line</td></tr>\n+ <tr><td class=param>Query length:</td><td>16</td></tr>\n+ <tr><td class=param>Program:</td><td>BLASTN 2.2.28+</td></tr>\n+ <tr><td class=param>Database:</td><td>/share/BlastDB/nt</td></tr>\n+ </table>\n+\n+ </section>\n+\n+ <section>\n+ <h2>No Hits</h2>\n+ <div class=grey>\n+ <table class=headerdata>\n+ <tr><td class=param>Message:</td><td>No hits found</td></tr>\n+ </table>\n+ </div>\n+ </section>\n+ </section>\n+\n+ </div>\n+\n+ <footer>\n+ This page was generated by <a href="...">blast2html</a>.\n+ </footer>\n+ </body>\n+</html>\n+\n' |
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| diff -r 344cd76f6fd2 -r ce8f29efc0a1 test-data/blast xml example3.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example3.html Thu May 15 17:22:02 2014 +0200 |
| b |
| b'@@ -0,0 +1,3530 @@\n+<!DOCTYPE html>\n+<html>\n+ <head>\n+ <meta charset="UTF-8">\n+ <meta name=generator content="blast2html; see ...">\n+ \n+ <title>Blast output</title>\n+ \n+ <style>\n+ body {\n+ color: #333333;\n+ font-family: Arial,Sans-Serif;\n+ }\n+\n+ :link {\n+ color: #336699;\n+ }\n+\n+ .right {\n+ float: right;\n+ }\n+\n+ /* Galaxy with html sanitization enabled strips the header of this html page. If so, show the user a warning.*/\n+ #strip_html_warning {\n+ display: none;\n+ }\n+ \n+ #content {\n+ margin: 0 2em;\n+ padding: 0.5em;\n+ border: 1px solid #888888;\n+ background-color: #d3dff5;\n+ }\n+\n+ h1, h2, h3, h4, h5, h6 {\n+ color: #2A6979;\n+ font-family: arial,verdana,sans-serif;\n+ letter-spacing: -1px;\n+ margin: 1.2em 0 0.3em;\n+ }\n+\n+ h1 {\n+ border-bottom: 1px solid #CCCCCC;\n+ font-size: 150%;\n+ padding-bottom: 0.1em;\n+ }\n+\n+ h2 {\n+ font-size: 120%;\n+ font-weight: bold;\n+ }\n+\n+ h4.darkHeader {\n+ color: #4D4D4D;\n+ letter-spacing: 0;\n+ font-weight: bold;\n+ }\n+\n+ #nodata {\n+ font-weight: bold;\n+ }\n+\n+ .index {\n+ margin-bottom: 3em;\n+ }\n+ .index div.indexentry {\n+ margin: 1.2em 1.6em;\n+ font-weight: bold;\n+ font-size: 100%;\n+ }\n+ \n+ .headerdata {\n+ font-size: 90%;\n+ }\n+ .headerdata .param {\n+ font-weight: bold;\n+ text-align: right;\n+ padding: 0 1em;\n+ }\n+\n+ .grey {\n+ background-color: #eeeeee;\n+ border: 1px solid #cccccc;\n+ padding: 1em;\n+ }\n+\n+ .white {\n+ background-color: white;\n+ border: 1px solid #cccccc;\n+ padding: 1.5em 2%;\n+ }\n+\n+ .graphicrow {\n+ clear: left;\n+ width: 100%;\n+ }\n+\n+ .graphicitem {\n+ float: left;\n+ }\n+\n+\n+ \n+ .graphics .grey {\n+ text-align: center;\n+ }\n+\n+ .graphic {\n+ background-color: white;\n+ border: 2px solid black;\n+ padding: 1.5em;\n+ margin: auto;\n+ }\n+\n+ .centered, .defline, div.legend, div.tablewrapper {\n+ margin-left: auto;\n+ margin-right: auto;\n+ }\n+\n+ .defline {\n+ background-color: white;\n+ border: 1px solid black;\n+ margin: .5em auto;\n+ padding-left: .2em;\n+ padding-right: .2em;\n+ max-width: 50em;\n+ text-align: left;\n+ height: 2.8em;\n+ overflow-y: hidden;\n+ }\n+\n+ div.legend {\n+ max-width: 40em;\n+ }\n+ div.legend div {\n+ width: 100%;\n+ color: white;\n+ font-weight: bold;\n+ border-spacing: 0;\n+ }\n+ div.legend div .graphicitem {\n+ width: 20%;\n+ padding: 0;\n+ margin: 0;\n+ border: none;\n+ }\n+\n+ div.tablewrapper {\n+ width: 50%;\n+ min-width: 60em;\n+ }\n+\n+ /* For small widths we give the graphic 100% */\n+ @media (max-width: 72.5em) {\n+ div.tablewrapper {\n+ width: 100%;\n+ min-width: 0px;\n+ }\n+ }\n+\n+ .scale {\n+ width: 100%;\n+ margin: .5em 0;\n+ font-weight: bold;\n+ }\n+ .scale div {\n+ color: red;\n+ text-align: left;\n+ }\n+ .scale .graphicrow {\n+ margin: .5em 0 .5em 0;\n+ color: white;\n+ }\n+ .scale .graphicitem {\n+ position: relative;\n+ }\n+ .scale .graphicitem div {\n+ margin: 0 1px;\n+ padding: 0 2px;\n+ text-align: right;\n+ background-color: red;\n+ color: white;\n+ }\n+ .scale .graphicitem:first-child div {\n+ margin-left: 0px;\n+ }\n+ .scale .graphicitem:last-child div {\n+ margin-right: 0px;\n+ }\n+ .scale .graphicitem .lastlabel {\n+ position: absolute;\n+ top: 0px;\n+ left: 100%;\n+ background-color: transparent;\n+ color: red;\n+ }\n+\n+ a.matchresult {\n+ display: block;\n+ margin: 0;\n+ padding:'..b' <h2>Descriptions</h2>\n+\n+ <div class=grey><div class=white>\n+ <h4 class=darkHeader>Sequences producing significant alignments:</h4>\n+\n+ <table class=descriptiontable>\n+ <col/><col/><col/><col/><col/><col/><col/>\n+ <tr>\n+ <th>Description</th>\n+ <th>Max score</th>\n+ <th>Total score</th>\n+ <th>Query cover</th>\n+ <th>E value</th>\n+ <th>Ident</th>\n+ <th>Accession</th>\n+ </tr>\n+ <tr>\n+ <td><div><a href="#hit1"\n+ title="EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000"\n+ id="description1">\n+ EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000\n+ </a></div></td>\n+ <td>89.7</td>\n+ <td>89.7</td>\n+ <td>100%</td>\n+ <td>6.629e-23</td>\n+ <td>86%</td>\n+ <td><a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a></td>\n+ </tr>\n+ </table>\n+\n+ </div></div>\n+ </section>\n+\n+\n+\n+ <section class=alignments>\n+ <h2>Alignments</h2>\n+\n+ <div class=grey><div class=white>\n+ <div class=alignment id=hit1>\n+\n+ <div class=linkheader>\n+ <div class=right><a href="#description1">Descriptions</a></div>\n+ <a class=linkheader href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">GenBank</a>\n+ <a class=linkheader href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=graph&log$=nuclalign">Graphics</a>\n+ </div>\n+\n+ <div class=title>\n+ <p class=hittitle>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</p>\n+ <p class=titleinfo>\n+ <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign">Subject_8</a>\n+ <span class=b>Length:</span> 4983\n+ <span class=b>Number of Matches:</span> 1\n+ </p>\n+ </div>\n+\n+\n+ <div class=hotspot>\n+ <p class=range>\n+ <span class=range>Range 1: 2319 to 2392</span>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=genbank&log$=nuclalign&from=2319&to=2392">GenBank</a>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/Subject_8?report=graph&log$=nuclalign&from=2319&to=2392">Graphics</a>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>89.7 bits(98)</td>\n+ <td>0.0</td>\n+ <td>64/74(86%)</td>\n+ <td>0/74(0%)</td>\n+ <td>Plus/Plus</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA 74\n+ ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||\n+Subject 2319 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA 2392</pre>\n+ </div>\n+\n+ </div>\n+\n+ </div></div>\n+ </section>\n+ </section>\n+\n+ </div>\n+\n+ <footer>\n+ This page was generated by <a href="...">blast2html</a>.\n+ </footer>\n+ </body>\n+</html>\n+\n' |
| b |
| diff -r 344cd76f6fd2 -r ce8f29efc0a1 test-data/blast xml example3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example3.xml Thu May 15 17:22:02 2014 +0200 |
| b |
| b'@@ -0,0 +1,1387 @@\n+<?xml version="1.0"?>\n+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n+<BlastOutput>\n+ <BlastOutput_program>blastn</BlastOutput_program>\n+ <BlastOutput_version>BLASTN 2.2.29+</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+ <BlastOutput_query-def>Forward_Primer|NOST-Spec_(Genetic_ID)</BlastOutput_query-def>\n+ <BlastOutput_query-len>20</BlastOutput_query-len>\n+ <BlastOutput_param>\n+ <Parameters>\n+ <Parameters_expect>0.001</Parameters_expect>\n+ <Parameters_sc-match>2</Parameters_sc-match>\n+ <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>\n+ <Parameters_gap-open>5</Parameters_gap-open>\n+ <Parameters_gap-extend>2</Parameters_gap-extend>\n+ <Parameters_filter>L;m;</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>\n+ <Iteration_query-len>20</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>8</Statistics_hsp-len>\n+ <Statistics_eff-space>12312</Statistics_eff-space>\n+ <Statistics_kappa>0.41</Statistics_kappa>\n+ <Statistics_lambda>0.625</Statistics_lambda>\n+ <Statistics_entropy>0.78</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>\n+ <Iteration_query-len>20</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>8</Statistics_hsp-len>\n+ <Statistics_eff-space>12312</Statistics_eff-space>\n+ <Statistics_kappa>0.41</Statistics_kappa>\n+ <Statistics_lambda>0.625</Statistics_lambda>\n+ <Statistics_entropy>0.78</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>\n+ <Iteration_query-len>20</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>Subject_3</Hit_id>\n+ <Hit_def>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</Hit_def>\n+ <Hit_accession>Subject_3</Hit_accession>\n+ <Hit_len>323</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>37.3537</Hsp_bit-score>\n+ <Hsp_score>40</Hsp_score>\n+ <Hsp_evalue>7.01052e-08</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>20</Hsp_query-to>\n+ <Hsp_hit-from>200</Hsp_hit-from>\n+ <Hsp_hit-to>219</Hsp_hit-to>\n+ <Hsp_query-frame>1</Hsp_query-frame>\n+ <Hsp_hit-frame>1</Hsp_hit-frame>\n+ <Hsp_identity>20</Hsp_identity>\n+ <Hsp_positive>20</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>20</Hsp_align-len>\n+ <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq>\n+ <Hsp_hseq>AGCGCGCAAACTAGGAT'..b'bda>\n+ <Statistics_entropy>0.78</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+ <Iteration_message>No hits found</Iteration_message>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>55</Iteration_iter-num>\n+ <Iteration_query-ID>Query_7</Iteration_query-ID>\n+ <Iteration_query-def>Amplicon|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>\n+ <Iteration_query-len>74</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>Subject_7</Hit_id>\n+ <Hit_def>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</Hit_def>\n+ <Hit_accession>Subject_7</Hit_accession>\n+ <Hit_len>4180</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>89.6514</Hsp_bit-score>\n+ <Hsp_score>98</Hsp_score>\n+ <Hsp_evalue>6.62923e-23</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>74</Hsp_query-to>\n+ <Hsp_hit-from>1516</Hsp_hit-from>\n+ <Hsp_hit-to>1589</Hsp_hit-to>\n+ <Hsp_query-frame>1</Hsp_query-frame>\n+ <Hsp_hit-frame>1</Hsp_hit-frame>\n+ <Hsp_identity>64</Hsp_identity>\n+ <Hsp_positive>64</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>74</Hsp_align-len>\n+ <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>\n+ <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>\n+ <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</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>11</Statistics_hsp-len>\n+ <Statistics_eff-space>64449</Statistics_eff-space>\n+ <Statistics_kappa>0.41</Statistics_kappa>\n+ <Statistics_lambda>0.625</Statistics_lambda>\n+ <Statistics_entropy>0.78</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>56</Iteration_iter-num>\n+ <Iteration_query-ID>Query_7</Iteration_query-ID>\n+ <Iteration_query-def>Amplicon|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>\n+ <Iteration_query-len>74</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>Subject_8</Hit_id>\n+ <Hit_def>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</Hit_def>\n+ <Hit_accession>Subject_8</Hit_accession>\n+ <Hit_len>4983</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>89.6514</Hsp_bit-score>\n+ <Hsp_score>98</Hsp_score>\n+ <Hsp_evalue>6.62923e-23</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>74</Hsp_query-to>\n+ <Hsp_hit-from>2319</Hsp_hit-from>\n+ <Hsp_hit-to>2392</Hsp_hit-to>\n+ <Hsp_query-frame>1</Hsp_query-frame>\n+ <Hsp_hit-frame>1</Hsp_hit-frame>\n+ <Hsp_identity>64</Hsp_identity>\n+ <Hsp_positive>64</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>74</Hsp_align-len>\n+ <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>\n+ <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>\n+ <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</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>11</Statistics_hsp-len>\n+ <Statistics_eff-space>64449</Statistics_eff-space>\n+ <Statistics_kappa>0.41</Statistics_kappa>\n+ <Statistics_lambda>0.625</Statistics_lambda>\n+ <Statistics_entropy>0.78</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+</BlastOutput_iterations>\n+</BlastOutput>\n+\n' |
| b |
| diff -r 344cd76f6fd2 -r ce8f29efc0a1 test-data/blast xml example4.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example4.html Thu May 15 17:22:02 2014 +0200 |
| b |
| b'@@ -0,0 +1,1606 @@\n+<!DOCTYPE html>\n+<html>\n+ <head>\n+ <meta charset="UTF-8">\n+ <meta name=generator content="blast2html; see ...">\n+ \n+ <title>Blast output</title>\n+ \n+ <style>\n+ body {\n+ color: #333333;\n+ font-family: Arial,Sans-Serif;\n+ }\n+\n+ :link {\n+ color: #336699;\n+ }\n+\n+ .right {\n+ float: right;\n+ }\n+\n+ /* Galaxy with html sanitization enabled strips the header of this html page. If so, show the user a warning.*/\n+ #strip_html_warning {\n+ display: none;\n+ }\n+ \n+ #content {\n+ margin: 0 2em;\n+ padding: 0.5em;\n+ border: 1px solid #888888;\n+ background-color: #d3dff5;\n+ }\n+\n+ h1, h2, h3, h4, h5, h6 {\n+ color: #2A6979;\n+ font-family: arial,verdana,sans-serif;\n+ letter-spacing: -1px;\n+ margin: 1.2em 0 0.3em;\n+ }\n+\n+ h1 {\n+ border-bottom: 1px solid #CCCCCC;\n+ font-size: 150%;\n+ padding-bottom: 0.1em;\n+ }\n+\n+ h2 {\n+ font-size: 120%;\n+ font-weight: bold;\n+ }\n+\n+ h4.darkHeader {\n+ color: #4D4D4D;\n+ letter-spacing: 0;\n+ font-weight: bold;\n+ }\n+\n+ #nodata {\n+ font-weight: bold;\n+ }\n+\n+ .index {\n+ margin-bottom: 3em;\n+ }\n+ .index div.indexentry {\n+ margin: 1.2em 1.6em;\n+ font-weight: bold;\n+ font-size: 100%;\n+ }\n+ \n+ .headerdata {\n+ font-size: 90%;\n+ }\n+ .headerdata .param {\n+ font-weight: bold;\n+ text-align: right;\n+ padding: 0 1em;\n+ }\n+\n+ .grey {\n+ background-color: #eeeeee;\n+ border: 1px solid #cccccc;\n+ padding: 1em;\n+ }\n+\n+ .white {\n+ background-color: white;\n+ border: 1px solid #cccccc;\n+ padding: 1.5em 2%;\n+ }\n+\n+ .graphicrow {\n+ clear: left;\n+ width: 100%;\n+ }\n+\n+ .graphicitem {\n+ float: left;\n+ }\n+\n+\n+ \n+ .graphics .grey {\n+ text-align: center;\n+ }\n+\n+ .graphic {\n+ background-color: white;\n+ border: 2px solid black;\n+ padding: 1.5em;\n+ margin: auto;\n+ }\n+\n+ .centered, .defline, div.legend, div.tablewrapper {\n+ margin-left: auto;\n+ margin-right: auto;\n+ }\n+\n+ .defline {\n+ background-color: white;\n+ border: 1px solid black;\n+ margin: .5em auto;\n+ padding-left: .2em;\n+ padding-right: .2em;\n+ max-width: 50em;\n+ text-align: left;\n+ height: 2.8em;\n+ overflow-y: hidden;\n+ }\n+\n+ div.legend {\n+ max-width: 40em;\n+ }\n+ div.legend div {\n+ width: 100%;\n+ color: white;\n+ font-weight: bold;\n+ border-spacing: 0;\n+ }\n+ div.legend div .graphicitem {\n+ width: 20%;\n+ padding: 0;\n+ margin: 0;\n+ border: none;\n+ }\n+\n+ div.tablewrapper {\n+ width: 50%;\n+ min-width: 60em;\n+ }\n+\n+ /* For small widths we give the graphic 100% */\n+ @media (max-width: 72.5em) {\n+ div.tablewrapper {\n+ width: 100%;\n+ min-width: 0px;\n+ }\n+ }\n+\n+ .scale {\n+ width: 100%;\n+ margin: .5em 0;\n+ font-weight: bold;\n+ }\n+ .scale div {\n+ color: red;\n+ text-align: left;\n+ }\n+ .scale .graphicrow {\n+ margin: .5em 0 .5em 0;\n+ color: white;\n+ }\n+ .scale .graphicitem {\n+ position: relative;\n+ }\n+ .scale .graphicitem div {\n+ margin: 0 1px;\n+ padding: 0 2px;\n+ text-align: right;\n+ background-color: red;\n+ color: white;\n+ }\n+ .scale .graphicitem:first-child div {\n+ margin-left: 0px;\n+ }\n+ .scale .graphicitem:last-child div {\n+ margin-right: 0px;\n+ }\n+ .scale .graphicitem .lastlabel {\n+ position: absolute;\n+ top: 0px;\n+ left: 100%;\n+ background-color: transparent;\n+ color: red;\n+ }\n+\n+ a.matchresult {\n+ display: block;\n+ margin: 0;\n+ padding:'..b' </div>\n+\n+\n+ <div class=hotspot>\n+ <p class=range>\n+ <span class=range>Range 1: 2319 to 2392</span>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/BL_ORD_ID?report=genbank&log$=nuclalign&from=2319&to=2392">GenBank</a>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/BL_ORD_ID?report=graph&log$=nuclalign&from=2319&to=2392">Graphics</a>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>67.9 bits(34)</td>\n+ <td>0.0</td>\n+ <td>64/74(86%)</td>\n+ <td>0/74(0%)</td>\n+ <td>Plus/Plus</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA 74\n+ ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||\n+Subject 2319 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA 2392</pre>\n+ </div>\n+\n+ </div>\n+\n+ <div class=alignment id=hit2>\n+\n+ <div class=linkheader>\n+ <div class=right><a href="#description2">Descriptions</a></div>\n+ <a class=linkheader href="http://www.ncbi.nlm.nih.gov/nucleotide/BL_ORD_ID?report=genbank&log$=nuclalign">GenBank</a>\n+ <a class=linkheader href="http://www.ncbi.nlm.nih.gov/nucleotide/BL_ORD_ID?report=graph&log$=nuclalign">Graphics</a>\n+ </div>\n+\n+ <div class=title>\n+ <p class=hittitle>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</p>\n+ <p class=titleinfo>\n+ <span class=b>Sequence ID:</span> <a href="http://www.ncbi.nlm.nih.gov/nucleotide/BL_ORD_ID?report=genbank&log$=nuclalign">6</a>\n+ <span class=b>Length:</span> 4180\n+ <span class=b>Number of Matches:</span> 1\n+ </p>\n+ </div>\n+\n+\n+ <div class=hotspot>\n+ <p class=range>\n+ <span class=range>Range 1: 1516 to 1589</span>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/BL_ORD_ID?report=genbank&log$=nuclalign&from=1516&to=1589">GenBank</a>\n+ <a class=range href="http://www.ncbi.nlm.nih.gov/nucleotide/BL_ORD_ID?report=graph&log$=nuclalign&from=1516&to=1589">Graphics</a>\n+ </p>\n+\n+ <table class=hotspotstable>\n+ <tr>\n+ <th>Score</th><th>Expect</th><th>Identities</th><th>Gaps</th><th>Strand</th>\n+ </tr>\n+ <tr>\n+ <td>67.9 bits(34)</td>\n+ <td>0.0</td>\n+ <td>64/74(86%)</td>\n+ <td>0/74(0%)</td>\n+ <td>Plus/Plus</td>\n+ </tr>\n+ </table>\n+\n+ <pre class=alignmentgraphic>Query 1 GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA 74\n+ ||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||\n+Subject 1516 GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA 1589</pre>\n+ </div>\n+\n+ </div>\n+\n+ </div></div>\n+ </section>\n+ </section>\n+\n+ </div>\n+\n+ <footer>\n+ This page was generated by <a href="...">blast2html</a>.\n+ </footer>\n+ </body>\n+</html>\n+\n' |
| b |
| diff -r 344cd76f6fd2 -r ce8f29efc0a1 test-data/blast xml example4.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/blast xml example4.xml Thu May 15 17:22:02 2014 +0200 |
| b |
| b'@@ -0,0 +1,412 @@\n+<?xml version="1.0"?>\n+<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">\n+<BlastOutput>\n+ <BlastOutput_program>blastn</BlastOutput_program>\n+ <BlastOutput_version>BLASTN 2.2.29+</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>/opt/galaxy/blastdbs/EUginius_plasmid_insert</BlastOutput_db>\n+ <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>\n+ <BlastOutput_query-def>Forward_Primer|NOST-Spec_(Genetic_ID)</BlastOutput_query-def>\n+ <BlastOutput_query-len>20</BlastOutput_query-len>\n+ <BlastOutput_param>\n+ <Parameters>\n+ <Parameters_expect>0.001</Parameters_expect>\n+ <Parameters_sc-match>1</Parameters_sc-match>\n+ <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>\n+ <Parameters_gap-open>5</Parameters_gap-open>\n+ <Parameters_gap-extend>2</Parameters_gap-extend>\n+ <Parameters_filter>L;m;</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>Forward_Primer|NOST-Spec_(Genetic_ID)</Iteration_query-def>\n+ <Iteration_query-len>20</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>gnl|BL_ORD_ID|5</Hit_id>\n+ <Hit_def>AB209952.1|GenBank|insert_GTS-40-3-2|Glycine_max_transgenic_cp4epsps_gene_for_5-enol-pyruvylshikimate-3-phospate_synthase_class_2_precursor,_complete_cds|-9105899556052450000</Hit_def>\n+ <Hit_accession>5</Hit_accession>\n+ <Hit_len>2457</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>40.14</Hsp_bit-score>\n+ <Hsp_score>20</Hsp_score>\n+ <Hsp_evalue>1.51296e-07</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>20</Hsp_query-to>\n+ <Hsp_hit-from>2119</Hsp_hit-from>\n+ <Hsp_hit-to>2138</Hsp_hit-to>\n+ <Hsp_query-frame>1</Hsp_query-frame>\n+ <Hsp_hit-frame>1</Hsp_hit-frame>\n+ <Hsp_identity>20</Hsp_identity>\n+ <Hsp_positive>20</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>20</Hsp_align-len>\n+ <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq>\n+ <Hsp_hseq>AGCGCGCAAACTAGGATAAA</Hsp_hseq>\n+ <Hsp_midline>||||||||||||||||||||</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+<Hit>\n+ <Hit_num>2</Hit_num>\n+ <Hit_id>gnl|BL_ORD_ID|2</Hit_id>\n+ <Hit_def>DJ437711|GenBank|insert_MIR604|Corn_Event_MIR604,_Left_Border_region|-5751164067366620000</Hit_def>\n+ <Hit_accession>2</Hit_accession>\n+ <Hit_len>323</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>40.14</Hsp_bit-score>\n+ <Hsp_score>20</Hsp_score>\n+ <Hsp_evalue>1.51296e-07</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>20</Hsp_query-to>\n+ <Hsp_hit-from>200</Hsp_hit-from>\n+ <Hsp_hit-to>219</Hsp_hit-to>\n+ <Hsp_query-frame>1</Hsp_query-frame>\n+ <Hsp_hit-frame>1</Hsp_hit-frame>\n+ <Hsp_identity>20</Hsp_identity>\n+ <Hsp_positive>20</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>20</Hsp_align-len>\n+ <Hsp_qseq>AGCGCGCAAACTAGGATAAA</Hsp_qseq>\n+ <Hsp_hseq>AGCGCGCAAACTAGGATAAA</Hsp_hseq>\n+ <Hsp_midline>||||||||||||||||||||</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>8</Statistics_db-num>\n+ <Statistics_db-len>15339</Statistics_db-len>\n+ <Statistics_hsp-len>8</Statistics_hsp-len>\n+ <Statistics_eff-space>183300</Statistics_eff-space>\n+ <Statistics_kappa>0.710602795216363</Statistics_kappa>\n+ <Statistics_la'..b'rame>\n+ <Hsp_identity>21</Hsp_identity>\n+ <Hsp_positive>21</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>22</Hsp_align-len>\n+ <Hsp_qseq>ACATGAACAGCGCCTTGACCAC</Hsp_qseq>\n+ <Hsp_hseq>ACATGAACAGCGCCCTGACCAC</Hsp_hseq>\n+ <Hsp_midline>|||||||||||||| |||||||</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>8</Statistics_db-num>\n+ <Statistics_db-len>15339</Statistics_db-len>\n+ <Statistics_hsp-len>9</Statistics_hsp-len>\n+ <Statistics_eff-space>244272</Statistics_eff-space>\n+ <Statistics_kappa>0.710602795216363</Statistics_kappa>\n+ <Statistics_lambda>1.37406312246009</Statistics_lambda>\n+ <Statistics_entropy>1.30724660390929</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+<Iteration>\n+ <Iteration_iter-num>7</Iteration_iter-num>\n+ <Iteration_query-ID>Query_7</Iteration_query-ID>\n+ <Iteration_query-def>Amplicon|QL-ELE-Bt-F1(mod)/Bt-R</Iteration_query-def>\n+ <Iteration_query-len>74</Iteration_query-len>\n+<Iteration_hits>\n+<Hit>\n+ <Hit_num>1</Hit_num>\n+ <Hit_id>gnl|BL_ORD_ID|7</Hit_id>\n+ <Hit_def>EUG|RIKILT|plasmid_pV-ZMBK07|plasmid_pV-ZMBK07|-2635190737607180000</Hit_def>\n+ <Hit_accession>7</Hit_accession>\n+ <Hit_len>4983</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>67.8929</Hsp_bit-score>\n+ <Hsp_score>34</Hsp_score>\n+ <Hsp_evalue>3.56369e-15</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>74</Hsp_query-to>\n+ <Hsp_hit-from>2319</Hsp_hit-from>\n+ <Hsp_hit-to>2392</Hsp_hit-to>\n+ <Hsp_query-frame>1</Hsp_query-frame>\n+ <Hsp_hit-frame>1</Hsp_hit-frame>\n+ <Hsp_identity>64</Hsp_identity>\n+ <Hsp_positive>64</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>74</Hsp_align-len>\n+ <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>\n+ <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>\n+ <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+<Hit>\n+ <Hit_num>2</Hit_num>\n+ <Hit_id>gnl|BL_ORD_ID|6</Hit_id>\n+ <Hit_def>AY326434|GenBank|insert_MON810|Synthetic_construct_truncated_CRYIA(b)_(cryIA(b))_gene,_partial_CDS|-2635190737607180000</Hit_def>\n+ <Hit_accession>6</Hit_accession>\n+ <Hit_len>4180</Hit_len>\n+ <Hit_hsps>\n+ <Hsp>\n+ <Hsp_num>1</Hsp_num>\n+ <Hsp_bit-score>67.8929</Hsp_bit-score>\n+ <Hsp_score>34</Hsp_score>\n+ <Hsp_evalue>3.56369e-15</Hsp_evalue>\n+ <Hsp_query-from>1</Hsp_query-from>\n+ <Hsp_query-to>74</Hsp_query-to>\n+ <Hsp_hit-from>1516</Hsp_hit-from>\n+ <Hsp_hit-to>1589</Hsp_hit-to>\n+ <Hsp_query-frame>1</Hsp_query-frame>\n+ <Hsp_hit-frame>1</Hsp_hit-frame>\n+ <Hsp_identity>64</Hsp_identity>\n+ <Hsp_positive>64</Hsp_positive>\n+ <Hsp_gaps>0</Hsp_gaps>\n+ <Hsp_align-len>74</Hsp_align-len>\n+ <Hsp_qseq>GAGGAAATGCGTATTCAATTCAACGACATGAACAGCGCCTTGACCACAGCTATCCCATTGTTCGCAGTCCAGAA</Hsp_qseq>\n+ <Hsp_hseq>GAGGAGATGCGCATCCAGTTCAACGACATGAACAGCGCCCTGACCACCGCCATCCCACTCTTCGCCGTCCAGAA</Hsp_hseq>\n+ <Hsp_midline>||||| ||||| || || ||||||||||||||||||||| ||||||| || |||||| | ||||| ||||||||</Hsp_midline>\n+ </Hsp>\n+ </Hit_hsps>\n+</Hit>\n+</Iteration_hits>\n+ <Iteration_stat>\n+ <Statistics>\n+ <Statistics_db-num>8</Statistics_db-num>\n+ <Statistics_db-len>15339</Statistics_db-len>\n+ <Statistics_hsp-len>10</Statistics_hsp-len>\n+ <Statistics_eff-space>976576</Statistics_eff-space>\n+ <Statistics_kappa>0.710602795216363</Statistics_kappa>\n+ <Statistics_lambda>1.37406312246009</Statistics_lambda>\n+ <Statistics_entropy>1.30724660390929</Statistics_entropy>\n+ </Statistics>\n+ </Iteration_stat>\n+</Iteration>\n+</BlastOutput_iterations>\n+</BlastOutput>\n+\n' |
| b |
| diff -r 344cd76f6fd2 -r ce8f29efc0a1 tool_dependencies.xml --- a/tool_dependencies.xml Thu May 15 16:59:18 2014 +0200 +++ b/tool_dependencies.xml Thu May 15 17:22:02 2014 +0200 |
| b |
| @@ -19,12 +19,20 @@ <tests> <test> - <param name="input" value="blast-view_test1_in.xml"/> - <output name="out_file1" file="blast-view_test1_out.html"/> + <param name="input" value="blast xml example1.xml"/> + <output name="out_file1" file="blast xml example1.html"/> </test> <test> - <param name="input" value="blast-view_test2_in.xml"/> - <output name="out_file1" file="blast-view_test2_out.html"/> + <param name="input" value="blast xml example2.xml"/> + <output name="out_file1" file="blast xml example2.html"/> + </test> + <test> + <param name="input" value="blast xml example3.xml"/> + <output name="out_file1" file="blast xml example3.html"/> + </test> + <test> + <param name="input" value="blast xml example4.xml"/> + <output name="out_file1" file="blast xml example4.html"/> </test> </tests> |