Mercurial > repos > jankanis > blast2html

annotate test-data/blast xml example2.xml @ 120:2729c2326235

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Fix for Rikilt issue 13 Hit e-value and identity% should be taken from the hsp with the highest bit score. Previously each of these values was calculated independently. Also use arrays for cover calculation instead of python lists and refactor the hit_info() code a bit.
author Jan Kanis <jan.code@jankanis.nl>
date Thu, 31 Jul 2014 16:14:36 +0200
parents 420d0508dcd6
children
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1 <?xml version="1.0"?>
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2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
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3 <BlastOutput>
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4 <BlastOutput_program>blastn</BlastOutput_program>
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5 <BlastOutput_version>BLASTN 2.2.28+</BlastOutput_version>
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6 <BlastOutput_reference>Stephen F. Altschul, Thomas L. Madden, Alejandro A. Sch&amp;auml;ffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), &quot;Gapped BLAST and PSI-BLAST: a new generation of protein database search programs&quot;, Nucleic Acids Res. 25:3389-3402.</BlastOutput_reference>
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7 <BlastOutput_db>/share/BlastDB/nt</BlastOutput_db>
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8 <BlastOutput_query-ID>Query_1</BlastOutput_query-ID>
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9 <BlastOutput_query-def>No definition line</BlastOutput_query-def>
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10 <BlastOutput_query-len>16</BlastOutput_query-len>
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11 <BlastOutput_param>
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12 <Parameters>
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13 <Parameters_expect>0.001</Parameters_expect>
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14 <Parameters_sc-match>2</Parameters_sc-match>
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15 <Parameters_sc-mismatch>-3</Parameters_sc-mismatch>
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16 <Parameters_gap-open>5</Parameters_gap-open>
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17 <Parameters_gap-extend>2</Parameters_gap-extend>
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18 <Parameters_filter>L;m;</Parameters_filter>
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19 </Parameters>
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20 </BlastOutput_param>
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21 <BlastOutput_iterations>
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22 <Iteration>
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23 <Iteration_iter-num>1</Iteration_iter-num>
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24 <Iteration_query-ID>Query_1</Iteration_query-ID>
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25 <Iteration_query-def>No definition line</Iteration_query-def>
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26 <Iteration_query-len>16</Iteration_query-len>
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27 <Iteration_hits>
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28 </Iteration_hits>
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29 <Iteration_stat>
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30 <Statistics>
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31 <Statistics_db-num>28813188</Statistics_db-num>
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32 <Statistics_db-len>53027764389</Statistics_db-len>
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33 <Statistics_hsp-len>13</Statistics_hsp-len>
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34 <Statistics_eff-space>157959578835</Statistics_eff-space>
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35 <Statistics_kappa>0.41</Statistics_kappa>
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36 <Statistics_lambda>0.625</Statistics_lambda>
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37 <Statistics_entropy>0.78</Statistics_entropy>
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38 </Statistics>
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39 </Iteration_stat>
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40 <Iteration_message>No hits found</Iteration_message>
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41 </Iteration>
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42 </BlastOutput_iterations>
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43 </BlastOutput>
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