Mercurial > repos > mheinzl > hd

annotate test-data/hd_output.tab @ 26:15d5da04ef70 draft

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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
author mheinzl
date Tue, 14 May 2019 03:48:39 -0400
parents 9e384b0741f1
children 6b15b3b6405c
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25
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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1 hd_data.tab
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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2 number of tags per file 20 (from 20) against 20
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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3
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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4 Hamming distance separated by family size
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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5 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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6 HD=1 5 1 1 1 1 0 9
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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7 HD=6 3 0 0 0 0 0 3
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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8 HD=7 4 0 0 0 1 0 5
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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9 HD=8 2 0 0 1 0 0 3
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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10 sum 14 1 1 2 2 0 20
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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11
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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12 Family size distribution separated by Hamming distance
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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13 HD=1 HD=2 HD=3 HD=4 HD=5-8 HD>8 sum
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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14 FS=1 5 0 0 0 9 0 14
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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15 FS=2 1 0 0 0 0 0 1
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16 FS=3 1 0 0 0 0 0 1
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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17 FS=4 1 0 0 0 1 0 2
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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18 FS=6 1 0 0 0 0 0 1
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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19 FS=7 0 0 0 0 1 0 1
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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20 sum 9 0 0 0 11 0 20
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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21
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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22
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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23 max. family size in sample: 7
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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24 absolute frequency: 1
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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25 relative frequency: 0.05
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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26
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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27 The Hamming distances were calculated by comparing the first halve against all halves and selected the minimum value (HD a).
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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28 For the second half of the tag, we compared them against all tags which resulted in the minimum HD of the previous step and selected the maximum value (HD b').
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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29 Finally, it was possible to calculate the absolute and relative differences between the HDs (absolute and relative delta HD).
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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30 These calculations were repeated, but starting with the second half in the first step to find all possible chimeras in the data (HD b and HD For simplicity we used the maximum value between the delta values in the end.
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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31 When only tags that can form DCS were allowed in the analysis, family sizes for the forward and reverse (ab and ba) will be included in the plots.
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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32 length of one part of the tag = 12
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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33
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34 Hamming distance of each half in the tag
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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35 HD a HD b' HD b HD a' HD a+b sum
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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36 HD=0 20 0 8 1 0 29
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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37 HD=1 0 0 1 19 8 28
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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38 HD=2 0 0 0 0 1 1
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39 HD=5 0 0 3 0 0 3
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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40 HD=6 0 0 2 0 3 5
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41 HD=7 0 1 6 0 4 11
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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42 HD=8 0 2 0 0 7 9
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43 HD=9 0 1 0 0 1 2
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44 HD=10 0 2 0 0 2 4
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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45 HD=11 0 7 0 0 7 14
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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46 HD=12 0 7 0 0 7 14
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47 sum 20 20 20 20 40 120
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48
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49 Absolute delta Hamming distances within the tag
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50 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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51 diff=7 1 0 0 0 0 0 1
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52 diff=8 1 0 0 0 1 0 2
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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53 diff=9 1 0 0 0 0 0 1
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54 diff=10 2 0 0 0 0 0 2
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55 diff=11 4 0 1 1 1 0 7
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56 diff=12 5 1 0 1 0 0 7
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57 sum 14 1 1 2 2 0 20
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58
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59 Chimera analysis: relative delta Hamming distances
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60 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
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61 diff=1.0 14 1 1 2 2 0 20
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62 sum 14 1 1 2 2 0 20
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63
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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64 Chimeras:
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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65 All tags were filtered: only those tags where at least one half was identical (HD=0) and therefore, had a relative delta of 1 were kept. These tags are considered as chimeric.
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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66 So the Hamming distances of the chimeric tags are shown.
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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67 Hamming distances of chimeras
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68 FS=1 FS=2 FS=3 FS=4 FS=5-10 FS>10 sum
9e384b0741f1 planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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69 HD=7 1 0 0 0 0 0 1
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70 HD=8 1 0 0 0 1 0 2
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71 HD=9 1 0 0 0 0 0 1
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72 HD=10 2 0 0 0 0 0 2
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73 HD=11 4 0 1 1 1 0 7
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74 HD=12 5 1 0 1 0 0 7
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75 sum 14 1 1 2 2 0 20
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76
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77