Mercurial > repos > mheinzl > hd
annotate hd.py @ 27:df1fc5cedc8b draft
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
author | mheinzl |
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date | Mon, 03 Jun 2019 05:15:27 -0400 |
parents | 9e384b0741f1 |
children | 1fa7342a140d |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1 #!/usr/bin/env python |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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2 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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3 # Hamming distance analysis of SSCSs |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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4 # |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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5 # Author: Monika Heinzl, Johannes-Kepler University Linz (Austria) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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6 # Contact: monika.heinzl@edumail.at |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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7 # |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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8 # Takes at least one TABULAR file with tags before the alignment to the SSCS and optionally a second TABULAR file as input. |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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9 # The program produces a plot which shows a histogram of Hamming distances separated after family sizes, |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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10 # a family size distribution separated after Hamming distances for all (sample_size=0) or a given sample of SSCSs or SSCSs, which form a DCS. |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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11 # In additon, the tool produces HD and FSD plots for the difference between the HDs of both parts of the tags and for the chimeric reads |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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12 # and finally a CSV file with the data of the plots. |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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13 # It is also possible to perform the HD analysis with shortened tags with given sizes as input. |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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14 # The tool can run on a certain number of processors, which can be defined by the user. |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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15 |
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7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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16 # USAGE: python hd.py --inputFile filename --inputName1 filename --sample_size int / |
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9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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17 # --only_DCS True --FamilySize3 True --subset_tag True --nproc int --minFS int --maxFS int --nr_above_bars True/False --output_tabular outptufile_name_tabular |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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18 |
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2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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19 import argparse |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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20 import itertools |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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21 import operator |
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2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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22 import sys |
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7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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23 from collections import Counter, defaultdict |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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24 from functools import partial |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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25 from multiprocessing.pool import Pool |
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9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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26 import random |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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27 import os |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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28 |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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29 import matplotlib.pyplot as plt |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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30 import numpy |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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31 from matplotlib.backends.backend_pdf import PdfPages |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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32 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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33 plt.switch_backend('agg') |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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34 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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35 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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36 def plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, originalCounts, |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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37 title_file1, subtitle, pdf, relative=False, diff=True): |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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38 if diff is False: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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39 colors = ["#e6194b", "#3cb44b", "#ffe119", "#0082c8", "#f58231", "#911eb4"] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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40 labels = ["HD=1", "HD=2", "HD=3", "HD=4", "HD=5-8", "HD>8"] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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41 else: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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42 colors = ["#93A6AB", "#403C14", "#731E41", "#BAB591", "#085B6F", "#E8AA35", "#726C66"] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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43 if relative is True: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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44 labels = ["d=0", "d=0.1", "d=0.2", "d=0.3", "d=0.4", "d=0.5-0.8", "d>0.8"] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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45 else: |
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46 labels = ["d=0", "d=1", "d=2", "d=3", "d=4", "d=5-8", "d>8"] |
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47 |
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48 fig = plt.figure(figsize=(6, 7)) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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49 ax = fig.add_subplot(111) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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50 plt.subplots_adjust(bottom=0.1) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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51 p1 = numpy.bincount(numpy.concatenate((familySizeList1))) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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52 maximumY = numpy.amax(p1) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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53 |
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54 if len(range(minimumXFS, maximumXFS)) == 0: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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55 range1 = range(minimumXFS - 1, minimumXFS + 2) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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56 else: |
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57 range1 = range(0, maximumXFS + 2) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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58 counts = plt.hist(familySizeList1, label=labels, |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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59 color=colors, stacked=True, |
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60 rwidth=0.8, alpha=1, align="left", |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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61 edgecolor="None", bins=range1) |
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62 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1)) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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63 |
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64 # plt.title(title_file1, fontsize=12) |
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65 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14) |
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66 plt.xlabel("Family size", fontsize=14) |
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67 plt.ylabel("Absolute Frequency", fontsize=14) |
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68 |
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69 ticks = numpy.arange(0, maximumXFS + 1, 1) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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70 ticks1 = map(str, ticks) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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71 if maximumXFS >= 20: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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72 ticks1[len(ticks1) - 1] = ">=20" |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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73 plt.xticks(numpy.array(ticks), ticks1) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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74 [l.set_visible(False) for (i, l) in enumerate(ax.get_xticklabels()) if i % 5 != 0] |
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75 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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76 plt.xlim((0, maximumXFS + 1)) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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77 if len(numpy.concatenate(familySizeList1)) != 0: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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78 plt.ylim((0, max(numpy.bincount(numpy.concatenate(familySizeList1))) * 1.1)) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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79 |
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80 plt.ylim((0, maximumY * 1.2)) |
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81 legend = "\nfamily size: \nabsolute frequency: \nrelative frequency: " |
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82 plt.text(0.15, -0.08, legend, size=12, transform=plt.gcf().transFigure) |
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83 |
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84 count = numpy.bincount(originalCounts) # original counts |
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85 if max(originalCounts) >= 20: |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
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86 max_count = ">= 20" |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
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87 else: |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
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88 max_count = max(originalCounts) |
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89 legend1 = "{}\n{}\n{:.5f}".format(max_count, count[len(count) - 1], float(count[len(count) - 1]) / sum(count)) |
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90 plt.text(0.5, -0.08, legend1, size=12, transform=plt.gcf().transFigure) |
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91 legend3 = "singletons\n{:,}\n{:.5f}".format(int(counts[0][len(counts[0]) - 1][1]), float(counts[0][len(counts[0]) - 1][1]) / sum(counts[0][len(counts[0]) - 1])) |
1
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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92 plt.text(0.7, -0.08, legend3, transform=plt.gcf().transFigure, size=12) |
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93 plt.grid(b=True, which='major', color='#424242', linestyle=':') |
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94 |
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95 pdf.savefig(fig, bbox_inches="tight") |
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96 plt.close("all") |
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97 |
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98 |
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99 def plotHDwithFSD(list1, maximumX, minimumX, subtitle, lenTags, title_file1, pdf, xlabel, relative=False, nr_above_bars=True, nr_unique_chimeras=0, len_sample=0): |
1
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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100 if relative is True: |
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101 step = 0.1 |
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102 else: |
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103 step = 1 |
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104 |
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105 fig = plt.figure(figsize=(6, 8)) |
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106 plt.subplots_adjust(bottom=0.1) |
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107 con_list1 = numpy.concatenate(list1) |
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108 p1 = numpy.array([v for k, v in sorted(Counter(con_list1).iteritems())]) |
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109 maximumY = numpy.amax(p1) |
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110 print("max X", maximumX, ) |
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111 |
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112 if relative is True: # relative difference |
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113 bin1 = numpy.arange(-1, maximumX + 0.2, 0.1) |
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114 else: |
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115 bin1 = maximumX + 1 |
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116 |
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117 counts = plt.hist(list1, bins=bin1, edgecolor='black', linewidth=1, |
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118 label=["FS=1", "FS=2", "FS=3", "FS=4", "FS=5-10", |
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119 "FS>10"], rwidth=0.8, |
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120 color=["#808080", "#FFFFCC", "#FFBF00", "#DF0101", "#0431B4", "#86B404"], |
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121 stacked=True, alpha=1, |
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122 align="left", |
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123 range=(0, maximumX + 1)) |
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124 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.45, 1)) |
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125 bins = counts[1] # width of bins |
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126 counts = numpy.array(map(int, counts[0][5])) |
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127 plt.suptitle(subtitle, y=1, x=0.5, fontsize=14) |
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128 # plt.title(title_file1, fontsize=12) |
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129 plt.xlabel(xlabel, fontsize=14) |
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130 plt.ylabel("Absolute Frequency", fontsize=14) |
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131 |
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132 plt.grid(b=True, which='major', color='#424242', linestyle=':') |
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133 plt.axis((minimumX - step, maximumX + step, 0, numpy.amax(counts) + sum(counts) * 0.1)) |
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134 plt.xticks(numpy.arange(0, maximumX + step, step)) |
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135 |
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136 plt.ylim((0, maximumY * 1.2)) |
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137 |
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138 if nr_above_bars is True: |
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139 bin_centers = -0.4 * numpy.diff(bins) + bins[:-1] |
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140 for x_label, label in zip(counts, bin_centers): # labels for values |
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141 if x_label == 0: |
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142 continue |
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143 else: |
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144 plt.annotate("{:,}\n{:.3f}".format(x_label, float(x_label) / sum(counts), 1), |
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145 xy=(label, x_label + len(con_list1) * 0.01), |
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146 xycoords="data", color="#000066", fontsize=10) |
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147 |
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148 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(lenTags, len_sample, sum(counts)) |
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149 plt.text(0.14, -0.05, legend, size=12, transform=plt.gcf().transFigure) |
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150 |
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151 # if nr_unique_chimeras != 0 and len_sample != 0: |
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152 # if relative == True: |
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153 # legend = "nr. of unique chimeric tags= {:,} ({:.5f}) (rel.diff=1)".format(nr_unique_chimeras, |
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154 # int(nr_unique_chimeras) / float(len_sample)) |
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155 # else: |
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156 # legend = "nr. of unique chimeric tags= {:,} ({:.5f})".format(nr_unique_chimeras, int(nr_unique_chimeras) / float(len_sample)) |
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157 # plt.text(0.14, -0.09, legend, size=12, transform=plt.gcf().transFigure) |
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158 |
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159 pdf.savefig(fig, bbox_inches="tight") |
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160 plt.close("all") |
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161 plt.clf() |
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162 |
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163 |
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164 def plotHDwithinSeq_Sum2(sum1, sum1min, sum2, sum2min, min_value, lenTags, title_file1, pdf, len_sample): |
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165 fig = plt.figure(figsize=(6, 8)) |
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166 plt.subplots_adjust(bottom=0.1) |
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167 |
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168 ham_partial = [sum1, sum1min, sum2, sum2min, numpy.array(min_value)] # new hd within tags |
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169 |
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170 maximumX = numpy.amax(numpy.concatenate(ham_partial)) |
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171 minimumX = numpy.amin(numpy.concatenate(ham_partial)) |
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172 maximumY = numpy.amax(numpy.array(numpy.concatenate(map(lambda x: numpy.bincount(x), ham_partial)))) |
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173 |
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174 if len(range(minimumX, maximumX)) == 0: |
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175 range1 = minimumX |
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176 else: |
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177 range1 = range(minimumX, maximumX + 2) |
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178 |
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179 plt.hist(ham_partial, align="left", rwidth=0.8, stacked=False, label=["HD a", "HD b'", "HD b", "HD a'", "HD a+b"], bins=range1, color=["#58ACFA", "#0404B4", "#FE642E", "#B40431", "#585858"], edgecolor='black', linewidth=1) |
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180 |
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181 plt.legend(loc='upper right', fontsize=14, frameon=True, bbox_to_anchor=(1.55, 1)) |
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182 plt.suptitle('Hamming distances within tags', fontsize=14) |
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183 # plt.title(title_file1, fontsize=12) |
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184 plt.xlabel("HD", fontsize=14) |
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185 plt.ylabel("Absolute Frequency", fontsize=14) |
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186 plt.grid(b=True, which='major', color='#424242', linestyle=':') |
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187 |
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188 plt.axis((minimumX - 1, maximumX + 1, 0, maximumY * 1.2)) |
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189 plt.xticks(numpy.arange(0, maximumX + 1, 1.0)) |
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190 # plt.ylim(0, maximumY * 1.2) |
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191 legend = "nr. of tags = {:,}\nsample size = {:,}\nnr. of data points = {:,}".format(lenTags, len_sample, len(numpy.concatenate(ham_partial))) |
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192 |
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193 # legend = "sample size= {:,} against {:,}".format(len(numpy.concatenate(ham_partial)), lenTags) |
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194 plt.text(0.14, -0.05, legend, size=12, transform=plt.gcf().transFigure) |
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195 pdf.savefig(fig, bbox_inches="tight") |
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196 plt.close("all") |
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197 plt.clf() |
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198 |
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199 |
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200 def createTableFSD2(list1, diff=True): |
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201 selfAB = numpy.concatenate(list1) |
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202 uniqueFS = numpy.unique(selfAB) |
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203 nr = numpy.arange(0, len(uniqueFS), 1) |
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204 if diff is False: |
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205 count = numpy.zeros((len(uniqueFS), 6)) |
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206 else: |
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207 count = numpy.zeros((len(uniqueFS), 7)) |
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208 |
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209 state = 1 |
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210 for i in list1: |
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211 counts = list(Counter(i).items()) |
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212 hd = [item[0] for item in counts] |
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213 c = [item[1] for item in counts] |
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214 table = numpy.column_stack((hd, c)) |
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215 if len(table) == 0: |
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216 state = state + 1 |
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217 continue |
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218 else: |
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219 if state == 1: |
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220 for i, l in zip(uniqueFS, nr): |
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221 for j in table: |
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222 if j[0] == uniqueFS[l]: |
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223 count[l, 0] = j[1] |
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224 if state == 2: |
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225 for i, l in zip(uniqueFS, nr): |
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226 for j in table: |
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227 if j[0] == uniqueFS[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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228 count[l, 1] = j[1] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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229 |
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230 if state == 3: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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231 for i, l in zip(uniqueFS, nr): |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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232 for j in table: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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233 if j[0] == uniqueFS[l]: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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234 count[l, 2] = j[1] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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235 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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236 if state == 4: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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237 for i, l in zip(uniqueFS, nr): |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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238 for j in table: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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239 if j[0] == uniqueFS[l]: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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240 count[l, 3] = j[1] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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241 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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242 if state == 5: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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243 for i, l in zip(uniqueFS, nr): |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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244 for j in table: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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245 if j[0] == uniqueFS[l]: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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246 count[l, 4] = j[1] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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247 |
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248 if state == 6: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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249 for i, l in zip(uniqueFS, nr): |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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250 for j in table: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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251 if j[0] == uniqueFS[l]: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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252 count[l, 5] = j[1] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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253 |
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254 if state == 7: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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255 for i, l in zip(uniqueFS, nr): |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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256 for j in table: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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257 if j[0] == uniqueFS[l]: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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258 count[l, 6] = j[1] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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259 state = state + 1 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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260 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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261 sumRow = count.sum(axis=1) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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262 sumCol = count.sum(axis=0) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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263 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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264 uniqueFS = uniqueFS.astype(str) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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265 if uniqueFS[len(uniqueFS) - 1] == "20": |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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266 uniqueFS[len(uniqueFS) - 1] = ">20" |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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267 |
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268 first = ["FS={}".format(i) for i in uniqueFS] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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269 final = numpy.column_stack((first, count, sumRow)) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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270 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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271 return (final, sumCol) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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272 |
19
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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273 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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274 def createFileFSD2(summary, sumCol, overallSum, output_file, name, sep, rel=False, diff=True): |
1
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275 output_file.write(name) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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276 output_file.write("\n") |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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277 if diff is False: |
19
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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278 output_file.write("{}HD=1{}HD=2{}HD=3{}HD=4{}HD=5-8{}HD>8{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep, sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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279 else: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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280 if rel is False: |
19
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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281 output_file.write("{}diff=0{}diff=1{}diff=2{}diff=3{}diff=4{}diff=5-8{}diff>8{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep, sep, sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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282 else: |
19
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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283 output_file.write("{}diff=0{}diff=0.1{}diff=0.2{}diff=0.3{}diff=0.4{}diff=0.5-0.8{}diff>0.8{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep, sep, sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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284 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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285 for item in summary: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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286 for nr in item: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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287 if "FS" not in nr and "diff" not in nr: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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288 nr = nr.astype(float) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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289 nr = nr.astype(int) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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290 output_file.write("{}{}".format(nr, sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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291 output_file.write("\n") |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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292 output_file.write("sum{}".format(sep)) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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293 sumCol = map(int, sumCol) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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294 for el in sumCol: |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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295 output_file.write("{}{}".format(el, sep)) |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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296 output_file.write("{}{}".format(overallSum.astype(int), sep)) |
1
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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297 output_file.write("\n\n") |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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298 |
19
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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299 |
1
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300 def createTableHD(list1, row_label): |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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301 selfAB = numpy.concatenate(list1) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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302 uniqueHD = numpy.unique(selfAB) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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303 nr = numpy.arange(0, len(uniqueHD), 1) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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304 count = numpy.zeros((len(uniqueHD), 6)) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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305 state = 1 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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306 for i in list1: |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
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307 counts = list(Counter(i).items()) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff
changeset
|
308 hd = [item[0] for item in counts] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff
changeset
|
309 c = [item[1] for item in counts] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff
changeset
|
310 table = numpy.column_stack((hd, c)) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff
changeset
|
311 if len(table) == 0: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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changeset
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312 state = state + 1 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff
changeset
|
313 continue |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
314 else: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
315 if state == 1: |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
316 for i, l in zip(uniqueHD, nr): |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
317 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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0
diff
changeset
|
318 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff
changeset
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319 count[l, 0] = j[1] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
320 if state == 2: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
321 for i, l in zip(uniqueHD, nr): |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
322 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
323 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff
changeset
|
324 count[l, 1] = j[1] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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diff
changeset
|
325 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
326 if state == 3: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
327 for i, l in zip(uniqueHD, nr): |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
328 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
329 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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changeset
|
330 count[l, 2] = j[1] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
331 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
332 if state == 4: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
333 for i, l in zip(uniqueHD, nr): |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
334 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
335 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
336 count[l, 3] = j[1] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
337 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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0
diff
changeset
|
338 if state == 5: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
339 for i, l in zip(uniqueHD, nr): |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
340 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
341 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
342 count[l, 4] = j[1] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
343 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
344 if state == 6: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
345 for i, l in zip(uniqueHD, nr): |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
346 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
347 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
348 count[l, 5] = j[1] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
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0
diff
changeset
|
349 state = state + 1 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
350 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
351 sumRow = count.sum(axis=1) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
352 sumCol = count.sum(axis=0) |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
353 first = ["{}{}".format(row_label, i) for i in uniqueHD] |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
354 final = numpy.column_stack((first, count, sumRow)) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
355 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
356 return (final, sumCol) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
357 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
358 |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
359 def createTableHDwithTags(list1): |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
360 selfAB = numpy.concatenate(list1) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
361 uniqueHD = numpy.unique(selfAB) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
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diff
changeset
|
362 nr = numpy.arange(0, len(uniqueHD), 1) |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
363 count = numpy.zeros((len(uniqueHD), 5)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
364 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
365 state = 1 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
366 for i in list1: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
367 counts = list(Counter(i).items()) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
368 hd = [item[0] for item in counts] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
369 c = [item[1] for item in counts] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
370 table = numpy.column_stack((hd, c)) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
371 if len(table) == 0: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
372 state = state + 1 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
373 continue |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
374 else: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
375 if state == 1: |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
376 for i, l in zip(uniqueHD, nr): |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
377 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
378 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
379 count[l, 0] = j[1] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
380 if state == 2: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
381 for i, l in zip(uniqueHD, nr): |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
382 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
383 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
384 count[l, 1] = j[1] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
385 if state == 3: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
386 for i, l in zip(uniqueHD, nr): |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
387 for j in table: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
388 if j[0] == uniqueHD[l]: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
389 count[l, 2] = j[1] |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
390 if state == 4: |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
391 for i, l in zip(uniqueHD, nr): |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
392 for j in table: |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
393 if j[0] == uniqueHD[l]: |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
394 count[l, 3] = j[1] |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
395 if state == 5: |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
396 for i, l in zip(uniqueHD, nr): |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
397 for j in table: |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
398 if j[0] == uniqueHD[l]: |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
399 count[l, 4] = j[1] |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
400 |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
401 state = state + 1 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
402 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
403 sumRow = count.sum(axis=1) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
404 sumCol = count.sum(axis=0) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
405 first = ["HD={}".format(i) for i in uniqueHD] |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
406 final = numpy.column_stack((first, count, sumRow)) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
407 |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
408 return (final, sumCol) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
409 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
410 |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
411 def createFileHD(summary, sumCol, overallSum, output_file, name, sep): |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
412 output_file.write(name) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
413 output_file.write("\n") |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
414 output_file.write("{}FS=1{}FS=2{}FS=3{}FS=4{}FS=5-10{}FS>10{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep, sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
415 for item in summary: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
416 for nr in item: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
417 if "HD" not in nr and "diff" not in nr: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
418 nr = nr.astype(float) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
419 nr = nr.astype(int) |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
420 output_file.write("{}{}".format(nr, sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
421 output_file.write("\n") |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
422 output_file.write("sum{}".format(sep)) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
423 sumCol = map(int, sumCol) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
424 for el in sumCol: |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
425 output_file.write("{}{}".format(el, sep)) |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
426 output_file.write("{}{}".format(overallSum.astype(int), sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
427 output_file.write("\n\n") |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
428 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
429 |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
430 def createFileHDwithinTag(summary, sumCol, overallSum, output_file, name, sep): |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
431 output_file.write(name) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
432 output_file.write("\n") |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
433 output_file.write("{}HD a{}HD b'{}HD b{}HD a'{}HD a+b{}sum{}\n".format(sep, sep, sep, sep, sep, sep, sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
434 for item in summary: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
435 for nr in item: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
436 if "HD" not in nr: |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
437 nr = nr.astype(float) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
438 nr = nr.astype(int) |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
439 output_file.write("{}{}".format(nr, sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
440 output_file.write("\n") |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
441 output_file.write("sum{}".format(sep)) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
442 sumCol = map(int, sumCol) |
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
443 for el in sumCol: |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
444 output_file.write("{}{}".format(el, sep)) |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
445 output_file.write("{}{}".format(overallSum.astype(int), sep)) |
1
7414792e1cb8
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 90ee23e393deb06fa5c15e3778fa23c39a25f7ce
mheinzl
parents:
0
diff
changeset
|
446 output_file.write("\n\n") |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
447 |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
448 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
449 def hamming(array1, array2): |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
450 res = 99 * numpy.ones(len(array1)) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
451 i = 0 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
452 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
453 for a in array1: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
454 dist = numpy.array([sum(itertools.imap(operator.ne, a, b)) for b in array2]) # fastest |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
455 res[i] = numpy.amin(dist[dist > 0]) # pick min distance greater than zero |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
456 # print(i) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
457 i += 1 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
458 return res |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
459 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
460 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
461 def hamming_difference(array1, array2, mate_b): |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
462 array2 = numpy.unique(array2) # remove duplicate sequences to decrease running time |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
changeset
|
463 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
464 array1_half = numpy.array([i[0:(len(i)) / 2] for i in array1]) # mate1 part1 |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
465 array1_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array1]) # mate1 part 2 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
466 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
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diff
changeset
|
467 array2_half = numpy.array([i[0:(len(i)) / 2] for i in array2]) # mate2 part1 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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468 array2_half2 = numpy.array([i[len(i) / 2:len(i)] for i in array2]) # mate2 part2 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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469 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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470 # diff11 = 999 * numpy.ones(len(array2)) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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471 # relativeDiffList = 999 * numpy.ones(len(array2)) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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472 # ham1 = 999 * numpy.ones(len(array2)) |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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473 # ham2 = 999 * numpy.ones(len(array2)) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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474 # min_valueList = 999 * numpy.ones(len(array2)) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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475 # min_tagsList = 999 * numpy.ones(len(array2)) |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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476 # diff11_zeros = 999 * numpy.ones(len(array2)) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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477 # min_tagsList_zeros = 999 * numpy.ones(len(array2)) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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478 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
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479 diff11 = [] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
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480 relativeDiffList = [] |
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481 ham1 = [] |
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482 ham2 = [] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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483 ham1min = [] |
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484 ham2min = [] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
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485 min_valueList = [] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
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486 min_tagsList = [] |
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487 diff11_zeros = [] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
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488 min_tagsList_zeros = [] |
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489 max_tag_list = [] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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490 i = 0 # counter, only used to see how many HDs of tags were already calculated |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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491 if mate_b is False: # HD calculation for all a's |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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492 half1_mate1 = array1_half |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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493 half2_mate1 = array1_half2 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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494 half1_mate2 = array2_half |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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495 half2_mate2 = array2_half2 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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496 elif mate_b is True: # HD calculation for all b's |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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497 half1_mate1 = array1_half2 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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498 half2_mate1 = array1_half |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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499 half1_mate2 = array2_half2 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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500 half2_mate2 = array2_half |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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501 # half1_mate1, index_halves = numpy.unique(half1_mate1, return_index=True) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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502 # print(len(half1_mate1)) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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503 # half2_mate1 = half2_mate1[index_halves] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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504 # array1 = array1[index_halves] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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505 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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506 for a, b, tag in zip(half1_mate1, half2_mate1, array1): |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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507 # exclude identical tag from array2, to prevent comparison to itself |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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508 sameTag = numpy.where(array2 == tag)[0] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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509 indexArray2 = numpy.arange(0, len(array2), 1) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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510 index_withoutSame = numpy.delete(indexArray2, sameTag) # delete identical tag from the data |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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511 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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512 # all tags without identical tag |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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513 array2_half_withoutSame = half1_mate2[index_withoutSame] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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514 array2_half2_withoutSame = half2_mate2[index_withoutSame] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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515 array2_withoutSame = array2[index_withoutSame] # whole tag (=not splitted into 2 halfs) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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516 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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517 dist = numpy.array([sum(itertools.imap(operator.ne, a, c)) for c in |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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518 array2_half_withoutSame]) # calculate HD of "a" in the tag to all "a's" or "b" in the tag to all "b's" |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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519 min_index = numpy.where(dist == dist.min())[0] # get index of min HD |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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520 min_value = dist.min() |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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521 # min_value = dist[min_index] # get minimum HDs |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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522 min_tag_half2 = array2_half2_withoutSame[min_index] # get all "b's" of the tag or all "a's" of the tag with minimum HD |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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523 min_tag_array2 = array2_withoutSame[min_index] # get whole tag with min HD |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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524 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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525 dist_second_half = numpy.array([sum(itertools.imap(operator.ne, b, e)) for e in min_tag_half2]) # calculate HD of "b" to all "b's" or "a" to all "a's" |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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526 max_value = dist_second_half.max() |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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527 max_index = numpy.where(dist_second_half == dist_second_half.max())[0] # get index of max HD |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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528 max_tag = min_tag_array2[max_index] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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529 |
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530 # for d, d2 in zip(min_value, max_value): |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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531 if mate_b is True: # half2, corrects the variable of the HD from both halfs if it is a or b |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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532 ham2.append(min_value) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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533 ham2min.append(max_value) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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534 else: # half1, corrects the variable of the HD from both halfs if it is a or b |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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535 ham1.append(min_value) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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536 ham1min.append(max_value) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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537 |
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538 min_valueList.append(min_value + max_value) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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539 min_tagsList.append(tag) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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540 difference1 = abs(min_value - max_value) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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541 diff11.append(difference1) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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542 rel_difference = round(float(difference1) / (min_value + max_value), 1) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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543 relativeDiffList.append(rel_difference) |
0
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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544 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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545 # tags which have identical parts: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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546 if min_value == 0 or max_value == 0: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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547 min_tagsList_zeros.append(numpy.array(tag)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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548 difference1_zeros = abs(min_value - max_value) # hd of non-identical part |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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549 diff11_zeros.append(difference1_zeros) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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550 max_tag_list.append(max_tag) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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551 else: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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552 min_tagsList_zeros.append(None) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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553 diff11_zeros.append(None) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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554 max_tag_list.append(numpy.array(["None"])) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
555 |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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556 # max_tag_list.append(numpy.array(max_tag)) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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557 |
8
e2596a4e1c56
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 24e245e913368abc55281d3bf22b2e1b8d60d26a
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558 i += 1 |
19
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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559 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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560 # print(i) |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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561 # diff11 = [st for st in diff11 if st != 999] |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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562 # ham1 = [st for st in ham1 if st != 999] |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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563 # ham2 = [st for st in ham2 if st != 999] |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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564 # min_valueList = [st for st in min_valueList if st != 999] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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565 # min_tagsList = [st for st in min_tagsList if st != 999] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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566 # relativeDiffList = [st for st in relativeDiffList if st != 999] |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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567 # diff11_zeros = [st for st in diff11_zeros if st != 999] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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568 # min_tagsList_zeros = [st for st in min_tagsList_zeros if st != 999] |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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569 return ([diff11, ham1, ham2, min_valueList, min_tagsList, relativeDiffList, diff11_zeros, min_tagsList_zeros, ham1min, ham2min, max_tag_list]) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
570 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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571 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
572 def readFileReferenceFree(file): |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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573 with open(file, 'r') as dest_f: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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574 data_array = numpy.genfromtxt(dest_f, skip_header=0, delimiter='\t', comments='#', dtype='string') |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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575 integers = numpy.array(data_array[:, 0]).astype(int) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
576 return(integers, data_array) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
577 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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578 |
11
7adc48c8a03d
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
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changeset
|
579 def hammingDistanceWithFS(fs, ham): |
7adc48c8a03d
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
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580 fs = numpy.asarray(fs) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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581 maximum = max(ham) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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582 minimum = min(ham) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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583 ham = numpy.asarray(ham) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
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changeset
|
584 |
11
7adc48c8a03d
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
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|
585 singletons = numpy.where(fs == 1)[0] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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586 data = ham[singletons] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
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changeset
|
587 |
11
7adc48c8a03d
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
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588 hd2 = numpy.where(fs == 2)[0] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
589 data2 = ham[hd2] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
590 |
11
7adc48c8a03d
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
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changeset
|
591 hd3 = numpy.where(fs == 3)[0] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
592 data3 = ham[hd3] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff
changeset
|
593 |
11
7adc48c8a03d
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
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changeset
|
594 hd4 = numpy.where(fs == 4)[0] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
595 data4 = ham[hd4] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff
changeset
|
596 |
11
7adc48c8a03d
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
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|
597 hd5 = numpy.where((fs >= 5) & (fs <= 10))[0] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
598 data5 = ham[hd5] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff
changeset
|
599 |
11
7adc48c8a03d
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 8d9bdadb5e154dadc455720c99700afbd9aafae9
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600 hd6 = numpy.where(fs > 10)[0] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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601 data6 = ham[hd6] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
602 |
239c4448a163
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603 list1 = [data, data2, data3, data4, data5, data6] |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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604 return(list1, maximum, minimum) |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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605 |
19
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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606 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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607 def familySizeDistributionWithHD(fs, ham, diff=False, rel=True): |
0
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608 hammingDistances = numpy.unique(ham) |
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609 fs = numpy.asarray(fs) |
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610 |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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611 ham = numpy.asarray(ham) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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612 bigFamilies2 = numpy.where(fs > 19)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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613 if len(bigFamilies2) != 0: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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614 fs[bigFamilies2] = 20 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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615 maximum = max(fs) |
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616 minimum = min(fs) |
239c4448a163
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617 if diff is True: |
239c4448a163
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618 hd0 = numpy.where(ham == 0)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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619 data0 = fs[hd0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
620 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
621 if rel is True: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
622 hd1 = numpy.where(ham == 0.1)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
623 else: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
624 hd1 = numpy.where(ham == 1)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
625 data = fs[hd1] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
626 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
627 if rel is True: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
628 hd2 = numpy.where(ham == 0.2)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
629 else: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
630 hd2 = numpy.where(ham == 2)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
631 data2 = fs[hd2] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
632 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
633 if rel is True: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
634 hd3 = numpy.where(ham == 0.3)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
635 else: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
636 hd3 = numpy.where(ham == 3)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
637 data3 = fs[hd3] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
638 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
639 if rel is True: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
640 hd4 = numpy.where(ham == 0.4)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
641 else: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
642 hd4 = numpy.where(ham == 4)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
643 data4 = fs[hd4] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
644 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
645 if rel is True: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
646 hd5 = numpy.where((ham >= 0.5) & (ham <= 0.8))[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
647 else: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
648 hd5 = numpy.where((ham >= 5) & (ham <= 8))[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
649 data5 = fs[hd5] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
650 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
651 if rel is True: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
652 hd6 = numpy.where(ham > 0.8)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
653 else: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
654 hd6 = numpy.where(ham > 8)[0] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
655 data6 = fs[hd6] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
656 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
657 if diff is True: |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
658 list1 = [data0, data, data2, data3, data4, data5, data6] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
659 else: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
660 list1 = [data, data2, data3, data4, data5, data6] |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
661 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
662 return(list1, hammingDistances, maximum, minimum) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
663 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
664 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
665 def make_argparser(): |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
666 parser = argparse.ArgumentParser(description='Hamming distance analysis of duplex sequencing data') |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
667 parser.add_argument('--inputFile', |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
668 help='Tabular File with three columns: ab or ba, tag and family size.') |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
669 parser.add_argument('--inputName1') |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
670 parser.add_argument('--sample_size', default=1000, type=int, |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
671 help='Sample size of Hamming distance analysis.') |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
672 parser.add_argument('--subset_tag', default=0, type=int, |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
673 help='The tag is shortened to the given number.') |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
674 parser.add_argument('--nproc', default=4, type=int, |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
675 help='The tool runs with the given number of processors.') |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
676 parser.add_argument('--only_DCS', action="store_false", |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
677 help='Only tags of the DCSs are included in the HD analysis') |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
678 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
679 parser.add_argument('--minFS', default=1, type=int, |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
680 help='Only tags, which have a family size greater or equal than specified, are included in the HD analysis') |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
681 parser.add_argument('--maxFS', default=0, type=int, |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
682 help='Only tags, which have a family size smaller or equal than specified, are included in the HD analysis') |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
683 parser.add_argument('--nr_above_bars', action="store_true", |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
changeset
|
684 help='If no, values above bars in the histograms are removed') |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
685 |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
686 parser.add_argument('--output_tabular', default="data.tabular", type=str, |
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
687 help='Name of the tabular file.') |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
688 parser.add_argument('--output_pdf', default="data.pdf", type=str, |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
689 help='Name of the pdf file.') |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
changeset
|
690 parser.add_argument('--output_chimeras_tabular', default="data.tabular", type=str, |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
21
diff
changeset
|
691 help='Name of the tabular file with all chimeric tags.') |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
changeset
|
692 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
693 return parser |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
694 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
mheinzl
parents:
18
diff
changeset
|
695 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
696 def Hamming_Distance_Analysis(argv): |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
changeset
|
697 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
698 parser = make_argparser() |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
699 args = parser.parse_args(argv[1:]) |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
changeset
|
700 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
701 file1 = args.inputFile |
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planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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702 name1 = args.inputName1 |
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9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
703 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
704 index_size = args.sample_size |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff
changeset
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705 title_savedFile_pdf = args.output_pdf |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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706 title_savedFile_csv = args.output_tabular |
22
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
707 output_chimeras_tabular = args.output_chimeras_tabular |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
708 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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709 sep = "\t" |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
710 onlyDuplicates = args.only_DCS |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
711 minFS = args.minFS |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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712 maxFS = args.maxFS |
14
883e6381ba29
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 38f5c032262361131c645812dd3dc639be6a5f4e
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|
713 nr_above_bars = args.nr_above_bars |
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9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
714 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
715 subset = args.subset_tag |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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716 nproc = args.nproc |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
717 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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718 # input checks |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff
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|
719 if index_size < 0: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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720 print("index_size is a negative integer.") |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
721 exit(2) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
722 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
723 if nproc <= 0: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff
changeset
|
724 print("nproc is smaller or equal zero") |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff
changeset
|
725 exit(3) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff
changeset
|
726 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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diff
changeset
|
727 if subset < 0: |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
728 print("subset_tag is smaller or equal zero.") |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff
changeset
|
729 exit(5) |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
730 |
19
2e9f7ea7ae93
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit dfaab79252a858e8df16bbea3607ebf1b6962e5a-dirty
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diff
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|
731 # PLOT |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff
changeset
|
732 plt.rcParams['axes.facecolor'] = "E0E0E0" # grey background color |
10
69aa17354a6e
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f01678e9bfead9f9e1b54dd9ecf7141f057dd9de
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parents:
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diff
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|
733 plt.rcParams['xtick.labelsize'] = 14 |
69aa17354a6e
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit f01678e9bfead9f9e1b54dd9ecf7141f057dd9de
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parents:
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diff
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|
734 plt.rcParams['ytick.labelsize'] = 14 |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
735 plt.rcParams['patch.edgecolor'] = "#000000" |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
736 plt.rc('figure', figsize=(11.69, 8.27)) # A4 format |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
737 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
738 name1 = name1.split(".tabular")[0] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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changeset
|
739 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
740 with open(title_savedFile_csv, "w") as output_file, PdfPages(title_savedFile_pdf) as pdf: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
741 print("dataset: ", name1) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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changeset
|
742 integers, data_array = readFileReferenceFree(file1) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
743 data_array = numpy.array(data_array) |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
744 print("total nr of tags with Ns:", len(data_array)) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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diff
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|
745 n = [i for i, x in enumerate(data_array[:, 1]) if "N" in x] |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
746 if len(n) != 0: # delete tags with N in the tag from data |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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diff
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|
747 print("nr of tags with N's within tag:", len(n), float(len(n)) / len(data_array)) |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
748 index_whole_array = numpy.arange(0, len(data_array), 1) |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
749 index_withoutN_inTag = numpy.delete(index_whole_array, n) |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
750 data_array = data_array[index_withoutN_inTag, :] |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
751 integers = integers[index_withoutN_inTag] |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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diff
changeset
|
752 print("total nr of tags without Ns:", len(data_array)) |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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diff
changeset
|
753 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
754 int_f = numpy.array(data_array[:, 0]).astype(int) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
755 data_array = data_array[numpy.where(int_f >= minFS)] |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
756 integers = integers[integers >= minFS] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
757 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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changeset
|
758 # select family size for tags |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
759 if maxFS > 0: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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diff
changeset
|
760 int_f2 = numpy.array(data_array[:, 0]).astype(int) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
761 data_array = data_array[numpy.where(int_f2 <= maxFS)] |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
762 integers = integers[integers <= maxFS] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
diff
changeset
|
763 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
764 if onlyDuplicates is True: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
765 tags = data_array[:, 2] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
766 seq = data_array[:, 1] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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diff
changeset
|
767 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
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|
768 # find all unique tags and get the indices for ALL tags, but only once |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
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changeset
|
769 u, index_unique, c = numpy.unique(numpy.array(seq), return_counts=True, return_index=True) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
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|
770 d = u[c > 1] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
771 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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diff
changeset
|
772 # get family sizes, tag for duplicates |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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changeset
|
773 duplTags_double = integers[numpy.in1d(seq, d)] |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
774 duplTags = duplTags_double[0::2] # ab of DCS |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
775 duplTagsBA = duplTags_double[1::2] # ba of DCS |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
776 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
777 duplTags_tag = tags[numpy.in1d(seq, d)][0::2] # ab |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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diff
changeset
|
778 duplTags_seq = seq[numpy.in1d(seq, d)][0::2] # ab - tags |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
779 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
changeset
|
780 if minFS > 1: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
changeset
|
781 duplTags_tag = duplTags_tag[(duplTags >= 3) & (duplTagsBA >= 3)] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
changeset
|
782 duplTags_seq = duplTags_seq[(duplTags >= 3) & (duplTagsBA >= 3)] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
changeset
|
783 duplTags = duplTags[(duplTags >= 3) & (duplTagsBA >= 3)] # ab+ba with FS>=3 |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
changeset
|
784 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
785 data_array = numpy.column_stack((duplTags, duplTags_seq)) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
786 data_array = numpy.column_stack((data_array, duplTags_tag)) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
787 integers = numpy.array(data_array[:, 0]).astype(int) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
788 print("DCS in whole dataset", len(data_array)) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
789 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
790 print("min FS", min(integers)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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|
791 print("max FS", max(integers)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
changeset
|
792 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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diff
changeset
|
793 # HD analysis for a subset of the tag |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
794 if subset > 0: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
795 tag1 = numpy.array([i[0:(len(i)) / 2] for i in data_array[:, 1]]) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
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796 tag2 = numpy.array([i[len(i) / 2:len(i)] for i in data_array[:, 1]]) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
797 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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|
798 flanking_region_float = float((len(tag1[0]) - subset)) / 2 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
799 flanking_region = int(flanking_region_float) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
800 if flanking_region_float % 2 == 0: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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diff
changeset
|
801 tag1_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag1]) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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diff
changeset
|
802 tag2_shorten = numpy.array([i[flanking_region:len(i) - flanking_region] for i in tag2]) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
803 else: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
804 flanking_region_rounded = int(round(flanking_region, 1)) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
805 flanking_region_rounded_end = len(tag1[0]) - subset - flanking_region_rounded |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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|
806 tag1_shorten = numpy.array( |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
807 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag1]) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
808 tag2_shorten = numpy.array( |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
809 [i[flanking_region:len(i) - flanking_region_rounded_end] for i in tag2]) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
810 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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changeset
|
811 data_array_tag = numpy.array([i + j for i, j in zip(tag1_shorten, tag2_shorten)]) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
812 data_array = numpy.column_stack((data_array[:, 0], data_array_tag, data_array[:, 2])) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
813 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
814 print("length of tag= ", len(data_array[0, 1])) |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
815 # select sample: if no size given --> all vs. all comparison |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
816 if index_size == 0: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
817 result = numpy.arange(0, len(data_array), 1) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
818 else: |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
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|
819 numpy.random.shuffle(data_array) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
changeset
|
820 unique_tags, unique_indices = numpy.unique(data_array[:, 1], return_index=True) # get only unique tags |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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diff
changeset
|
821 result = numpy.random.choice(unique_indices, size=index_size, replace=False) # array of random sequences of size=index.size |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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diff
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|
822 |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
changeset
|
823 # result = numpy.random.choice(len(integers), size=index_size, |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
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|
824 # replace=False) # array of random sequences of size=index.size |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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diff
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|
825 # result = numpy.where(numpy.array(random_tags) == numpy.array(data_array[:,1]))[0] |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
826 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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diff
changeset
|
827 # with open("index_result1_{}.pkl".format(app_f), "wb") as o: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
828 # pickle.dump(result, o, pickle.HIGHEST_PROTOCOL) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
829 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
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|
830 # comparison random tags to whole dataset |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
831 result1 = data_array[result, 1] # random tags |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
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|
832 result2 = data_array[:, 1] # all tags |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
833 print("sample size= ", len(result1)) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
834 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
835 # HD analysis of whole tag |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
836 proc_pool = Pool(nproc) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
837 chunks_sample = numpy.array_split(result1, nproc) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
838 ham = proc_pool.map(partial(hamming, array2=result2), chunks_sample) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
839 proc_pool.close() |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
840 proc_pool.join() |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
841 ham = numpy.concatenate(ham).astype(int) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
842 # with open("HD_whole dataset_{}.txt".format(app_f), "w") as output_file1: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
843 # for h, tag in zip(ham, result1): |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
844 # output_file1.write("{}\t{}\n".format(tag, h)) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
845 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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diff
changeset
|
846 # # HD analysis for chimeric reads |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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changeset
|
847 # result2 = data_array_whole_dataset[:,1] |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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changeset
|
848 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
849 proc_pool_b = Pool(nproc) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
850 diff_list_a = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=False), chunks_sample) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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851 diff_list_b = proc_pool_b.map(partial(hamming_difference, array2=result2, mate_b=True), chunks_sample) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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852 proc_pool_b.close() |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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853 proc_pool_b.join() |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
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854 HDhalf1 = numpy.concatenate((numpy.concatenate([item[1] for item in diff_list_a]), |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
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855 numpy.concatenate([item_b[1] for item_b in diff_list_b]))).astype(int) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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changeset
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856 HDhalf2 = numpy.concatenate((numpy.concatenate([item[2] for item in diff_list_a]), |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
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857 numpy.concatenate([item_b[2] for item_b in diff_list_b]))).astype(int) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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858 minHDs = numpy.concatenate((numpy.concatenate([item[3] for item in diff_list_a]), |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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859 numpy.concatenate([item_b[3] for item_b in diff_list_b]))).astype(int) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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changeset
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860 HDhalf1min = numpy.concatenate((numpy.concatenate([item[8] for item in diff_list_a]), |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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changeset
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861 numpy.concatenate([item_b[8] for item_b in diff_list_b]))).astype(int) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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changeset
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862 HDhalf2min = numpy.concatenate((numpy.concatenate([item[9] for item in diff_list_a]), |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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863 numpy.concatenate([item_b[9] for item_b in diff_list_b]))).astype(int) |
0
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864 |
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865 rel_Diff1 = numpy.concatenate([item[5] for item in diff_list_a]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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866 rel_Diff2 = numpy.concatenate([item[5] for item in diff_list_b]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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867 diff1 = numpy.concatenate([item[0] for item in diff_list_a]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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868 diff2 = numpy.concatenate([item[0] for item in diff_list_b]) |
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7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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869 |
25
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870 diff_zeros1 = numpy.concatenate([item[6] for item in diff_list_a]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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871 diff_zeros2 = numpy.concatenate([item[6] for item in diff_list_b]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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872 minHD_tags = numpy.concatenate([item[4] for item in diff_list_a]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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873 minHD_tags_zeros1 = numpy.concatenate([item[7] for item in diff_list_a]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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874 minHD_tags_zeros2 = numpy.concatenate([item[7] for item in diff_list_b]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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875 chim_tags = [item[10] for item in diff_list_a] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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876 chim_tags2 = [item[10] for item in diff_list_b] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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877 chimera_tags1 = [ii if isinstance(i, list) else i for i in chim_tags for ii in i] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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878 chimera_tags2 = [ii if isinstance(i, list) else i for i in chim_tags2 for ii in i] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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879 |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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880 rel_Diff = [] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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881 diff_zeros = [] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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882 minHD_tags_zeros = [] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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883 diff = [] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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884 chimera_tags = [] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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885 for d1, d2, rel1, rel2, zeros1, zeros2, tag1, tag2, ctag1, ctag2 in \ |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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886 zip(diff1, diff2, rel_Diff1, rel_Diff2, diff_zeros1, diff_zeros2, minHD_tags_zeros1, minHD_tags_zeros2, chimera_tags1, chimera_tags2): |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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887 rel_Diff.append(max(rel1, rel2)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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888 diff.append(max(d1, d2)) |
22
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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889 |
25
9e384b0741f1
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890 if all(i is not None for i in [zeros1, zeros2]): |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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891 diff_zeros.append(max(zeros1, zeros2)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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892 minHD_tags_zeros.append(str(tag1)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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893 tags = [ctag1, ctag2] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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894 chimera_tags.append(tags) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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895 elif zeros1 is not None and zeros2 is None: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
896 diff_zeros.append(zeros1) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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897 minHD_tags_zeros.append(str(tag1)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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898 chimera_tags.append(ctag1) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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899 elif zeros1 is None and zeros2 is not None: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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900 diff_zeros.append(zeros2) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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901 minHD_tags_zeros.append(str(tag2)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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902 chimera_tags.append(ctag2) |
22
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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903 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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904 chimera_tags_new = chimera_tags |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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905 #data_chimeraAnalysis = numpy.column_stack((minHD_tags_zeros, chimera_tags_new)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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906 # chimeras_dic = defaultdict(list) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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907 # |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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908 # for t1, t2 in zip(minHD_tags_zeros, chimera_tags_new): |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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909 # if len(t2) >1 and type(t2) is not numpy.ndarray: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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910 # t2 = numpy.concatenate(t2) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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911 # chimeras_dic[t1].append(t2) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
912 |
22
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913 with open(output_chimeras_tabular, "w") as output_file1: |
25
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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914 output_file1.write("chimera tag\tsimilar tag with HD=0\n") |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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915 for i in range(len(minHD_tags_zeros)): |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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916 tag1 = minHD_tags_zeros[i] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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917 sample_half_a = tag1[0:(len(tag1)) / 2] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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918 sample_half_b = tag1[len(tag1) / 2:len(tag1)] |
22
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|
919 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
920 max_tags = chimera_tags_new[i] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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|
921 if isinstance(max_tags, list) and len(max_tags) > 1: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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diff
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|
922 max_tags = numpy.concatenate(max_tags) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
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|
923 #if isinstance(max_tags, list): #and type(max_tags) is not numpy.ndarray: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
924 # print(max_tags) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
925 # max_tags = numpy.concatenate(max_tags) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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diff
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|
926 max_tags = numpy.unique(max_tags) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
927 |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
928 chimera_half_a = numpy.array([i[0:(len(i)) / 2] for i in max_tags]) # mate1 part1 |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
929 chimera_half_b = numpy.array([i[len(i) / 2:len(i)] for i in max_tags]) # mate1 part 2 |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
930 |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
931 new_format = [] |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
932 for j in range(len(max_tags)): |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
933 if sample_half_a == chimera_half_a[j]: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
934 max_tag = "*{}* {}".format(chimera_half_a[j], chimera_half_b[j]) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
935 new_format.append(max_tag) |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
936 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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parents:
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|
937 elif sample_half_b == chimera_half_b[j]: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
938 max_tag = "{} *{}*".format(chimera_half_a[j], chimera_half_b[j]) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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|
939 new_format.append(max_tag) |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
940 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
941 sample_tag = "{} {}".format(sample_half_a, sample_half_b) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
942 output_file1.write("{}\t{}\n".format(sample_tag, ", ".join(new_format))) |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
943 output_file1.write( |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
944 "This file contains all tags that were identified as chimeras as the first column and the corresponding tags which returned a Hamming distance of zero in either the first or the second half of the sample tag as the second column.\n " |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
945 "The tags were separated by an empty space into their halves and the * marks the identical half.") |
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
946 |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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parents:
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diff
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|
947 # unique_chimeras = numpy.array(minHD_tags_zeros) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
948 # |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
949 # sample_half_a = numpy.array([i[0:(len(i)) / 2] for i in unique_chimeras]) # mate1 part1 |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
950 # sample_half_b = numpy.array([i[len(i) / 2:len(i)] for i in unique_chimeras]) # mate1 part 2 |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
951 # |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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|
952 # output_file1.write("sample tag\tsimilar tag\n") |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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diff
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|
953 # for tag1, a, b in zip(unique_chimeras, sample_half_a, sample_half_b): |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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22
diff
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|
954 # max_tags = numpy.concatenate(chimeras_dic.get(tag1)) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
955 # max_tags = numpy.unique(max_tags) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
956 # |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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diff
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|
957 # chimera_half_a = numpy.array([i[0:(len(i)) / 2] for i in max_tags]) # mate1 part1 |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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diff
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|
958 # chimera_half_b = numpy.array([i[len(i) / 2:len(i)] for i in max_tags]) # mate1 part 2 |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
959 # |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
960 # new_format = [] |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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diff
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|
961 # for i in range(len(max_tags)): |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
22
diff
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|
962 # if a == chimera_half_a[i]: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
963 # max_tag = "*{}* {}".format(chimera_half_a[i], chimera_half_b[i]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
964 # new_format.append(max_tag) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
965 # |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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diff
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|
966 # elif b == chimera_half_b[i]: |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
967 # max_tag = "{} *{}*".format(chimera_half_a[i], chimera_half_b[i]) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
968 # new_format.append(max_tag) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
969 # |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
970 # sample_tag = "{} {}".format(a, b) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
971 # output_file1.write("{}\t{}\n".format(sample_tag, ", ".join(new_format))) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
972 # output_file1.write( |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
973 # "This file contains all tags that were identified as chimeras as the first column and the corresponding tags which returned a Hamming distance of zero in either the first or the second half of the sample tag as the second column.\n " |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
parents:
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|
974 # "The tags were separated by an empty space into their halves and the * marks the identical half.") |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
975 |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
976 nr_chimeric_tags = len(minHD_tags_zeros) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
977 print("nr of unique chimeras", nr_chimeric_tags) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
978 |
20
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
979 lenTags = len(data_array) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
980 len_sample = len(result1) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
981 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
982 quant = numpy.array(data_array[result, 0]).astype(int) # family size for sample of tags |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
983 seq = numpy.array(data_array[result, 1]) # tags of sample |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
984 ham = numpy.asarray(ham) # HD for sample of tags |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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|
985 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
986 if onlyDuplicates is True: # ab and ba strands of DCSs |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
987 quant = numpy.concatenate((quant, duplTagsBA[result])) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
988 seq = numpy.tile(seq, 2) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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989 ham = numpy.tile(ham, 2) |
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990 diff = numpy.tile(diff, 2) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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991 rel_Diff = numpy.tile(rel_Diff, 2) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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992 diff_zeros = numpy.tile(diff_zeros, 2) |
0
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993 |
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994 # prepare data for different kinds of plots |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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995 # distribution of FSs separated after HD |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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996 familySizeList1, hammingDistances, maximumXFS, minimumXFS = familySizeDistributionWithHD(quant, ham, rel=False) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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997 list1, maximumX, minimumX = hammingDistanceWithFS(quant, ham) # histogram of HDs separated after FS |
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998 |
20
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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999 # get FS for all tags with min HD of analysis of chimeric reads |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1000 # there are more tags than sample size in the plot, because one tag can have multiple minimas |
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1001 if onlyDuplicates: |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1002 seqDic = defaultdict(list) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1003 for s, q in zip(seq, quant): |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1004 seqDic[s].append(q) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1005 else: |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1006 seqDic = dict(zip(seq, quant)) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1007 |
20
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1008 lst_minHD_tags = [] |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1009 for i in minHD_tags: |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1010 lst_minHD_tags.append(seqDic.get(i)) |
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1011 |
22
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1012 if onlyDuplicates: |
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1013 lst_minHD_tags = numpy.concatenate(([item[0] for item in lst_minHD_tags], [item_b[1] for item_b in lst_minHD_tags])).astype(int) |
22
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1014 |
20
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1015 # histogram with absolute and relative difference between HDs of both parts of the tag |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1016 listDifference1, maximumXDifference, minimumXDifference = hammingDistanceWithFS(lst_minHD_tags, diff) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1017 listRelDifference1, maximumXRelDifference, minimumXRelDifference = hammingDistanceWithFS(lst_minHD_tags, |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1018 rel_Diff) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1019 # chimeric read analysis: tags which have HD=0 in one of the halfs |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1020 if len(minHD_tags_zeros) != 0: |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1021 lst_minHD_tags_zeros = [] |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1022 for i in minHD_tags_zeros: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1023 lst_minHD_tags_zeros.append(seqDic.get(i)) # get family size for tags of chimeric reads |
22
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1024 if onlyDuplicates: |
25
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1025 lst_minHD_tags_zeros = numpy.concatenate(([item[0] for item in lst_minHD_tags_zeros], [item_b[1] for item_b in lst_minHD_tags_zeros])).astype(int) |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1026 |
22
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|
1027 # histogram with HD of non-identical half |
25
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1028 listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros = hammingDistanceWithFS(lst_minHD_tags_zeros, diff_zeros) |
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1029 |
20
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|
1030 # plot Hamming Distance with Family size distribution |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1031 plotHDwithFSD(list1=list1, maximumX=maximumX, minimumX=minimumX, pdf=pdf, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1032 subtitle="Hamming distance separated by family size", title_file1=name1, lenTags=lenTags, |
25
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1033 xlabel="HD", nr_above_bars=nr_above_bars, len_sample=len_sample) |
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1034 |
20
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1035 # Plot FSD with separation after |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1036 plotFSDwithHD2(familySizeList1, maximumXFS, minimumXFS, |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1037 originalCounts=quant, subtitle="Family size distribution separated by Hamming distance", |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1038 pdf=pdf, relative=False, title_file1=name1, diff=False) |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
1039 |
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1040 # Plot HD within tags |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1041 plotHDwithinSeq_Sum2(HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, minHDs, pdf=pdf, lenTags=lenTags, |
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1042 title_file1=name1, len_sample=len_sample) |
0
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1043 |
20
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1044 # Plot difference between HD's separated after FSD |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1045 plotHDwithFSD(listDifference1, maximumXDifference, minimumXDifference, pdf=pdf, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1046 subtitle="Delta Hamming distance within tags", |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1047 title_file1=name1, lenTags=lenTags, |
25
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1048 xlabel="absolute delta HD", relative=False, nr_above_bars=nr_above_bars, len_sample=len_sample) |
0
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1049 |
20
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1050 plotHDwithFSD(listRelDifference1, maximumXRelDifference, minimumXRelDifference, pdf=pdf, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1051 subtitle="Chimera Analysis: relative delta Hamming distances", |
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
1052 title_file1=name1, lenTags=lenTags, |
22
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|
1053 xlabel="relative delta HD", relative=True, nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample) |
0
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1054 |
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|
1055 # plots for chimeric reads |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1056 if len(minHD_tags_zeros) != 0: |
19
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1057 # HD |
25
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1058 plotHDwithFSD(listDifference1_zeros, maximumXDifference_zeros, minimumXDifference_zeros, pdf=pdf, subtitle="Hamming distance of chimeras", |
20
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1059 title_file1=name1, lenTags=lenTags, xlabel="HD", relative=False, |
22
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
1060 nr_above_bars=nr_above_bars, nr_unique_chimeras=nr_chimeric_tags, len_sample=len_sample) |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1061 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1062 # print all data to a CSV file |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1063 # HD |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1064 summary, sumCol = createTableHD(list1, "HD=") |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1065 overallSum = sum(sumCol) # sum of columns in table |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1066 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1067 # FSD |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1068 summary5, sumCol5 = createTableFSD2(familySizeList1, diff=False) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1069 overallSum5 = sum(sumCol5) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1070 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1071 # HD of both parts of the tag |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1072 summary9, sumCol9 = createTableHDwithTags([HDhalf1, HDhalf1min, HDhalf2, HDhalf2min, numpy.array(minHDs)]) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1073 overallSum9 = sum(sumCol9) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1074 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1075 # HD |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1076 # absolute difference |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1077 summary11, sumCol11 = createTableHD(listDifference1, "diff=") |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1078 overallSum11 = sum(sumCol11) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1079 # relative difference and all tags |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1080 summary13, sumCol13 = createTableHD(listRelDifference1, "diff=") |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1081 overallSum13 = sum(sumCol13) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1082 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1083 # chimeric reads |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1084 if len(minHD_tags_zeros) != 0: |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1085 # absolute difference and tags where at least one half has HD=0 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1086 summary15, sumCol15 = createTableHD(listDifference1_zeros, "HD=") |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1087 overallSum15 = sum(sumCol15) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
|
1088 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1089 output_file.write("{}\n".format(name1)) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1090 output_file.write("number of tags per file{}{:,} (from {:,}) against {:,}\n\n".format(sep, len( |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1091 numpy.concatenate(list1)), lenTags, lenTags)) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1092 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1093 # HD |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1094 createFileHD(summary, sumCol, overallSum, output_file, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
19
diff
changeset
|
1095 "Hamming distance separated by family size", sep) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1096 # FSD |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1097 createFileFSD2(summary5, sumCol5, overallSum5, output_file, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1098 "Family size distribution separated by Hamming distance", sep, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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diff
changeset
|
1099 diff=False) |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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1100 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
1101 # output_file.write("{}{}\n".format(sep, name1)) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1102 output_file.write("\n") |
21
9919024d7778
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
mheinzl
parents:
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|
1103 max_fs = numpy.bincount(integers[result]) |
9919024d7778
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
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parents:
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changeset
|
1104 output_file.write("max. family size in sample:{}{}\n".format(sep, max(integers[result]))) |
9919024d7778
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
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changeset
|
1105 output_file.write("absolute frequency:{}{}\n".format(sep, max_fs[len(max_fs) - 1])) |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1106 output_file.write( |
21
9919024d7778
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6
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parents:
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|
1107 "relative frequency:{}{}\n\n".format(sep, float(max_fs[len(max_fs) - 1]) / sum(max_fs))) |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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changeset
|
1108 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1109 # HD within tags |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
1110 output_file.write( |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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parents:
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|
1111 "The Hamming distances were calculated by comparing the first halve against all halves and selected the minimum value (HD a).\n" |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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|
1112 "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').\n" |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
1113 "Finally, it was possible to calculate the absolute and relative differences between the HDs (absolute and relative delta HD).\n" |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1114 "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.\n" |
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
1115 "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.\n") |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1116 |
20
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planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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|
1117 output_file.write("length of one part of the tag = {}\n\n".format(len(data_array[0, 1]) / 2)) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
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1118 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
1119 createFileHDwithinTag(summary9, sumCol9, overallSum9, output_file, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1120 "Hamming distance of each half in the tag", sep) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
1121 createFileHD(summary11, sumCol11, overallSum11, output_file, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1122 "Absolute delta Hamming distances within the tag", sep) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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1123 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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parents:
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|
1124 createFileHD(summary13, sumCol13, overallSum13, output_file, |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1125 "Chimera analysis: relative delta Hamming distances", sep) |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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changeset
|
1126 |
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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|
1127 if len(minHD_tags_zeros) != 0: |
0
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
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parents:
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|
1128 output_file.write( |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
1129 "Chimeras:\nAll 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.\nSo the Hamming distances of the chimeric tags are shown.\n") |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
mheinzl
parents:
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1130 createFileHD(summary15, sumCol15, overallSum15, output_file, |
25
9e384b0741f1
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
mheinzl
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changeset
|
1131 "Hamming distances of chimeras", sep) |
22
7e570ba56b83
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit b8a2f7b7615b2bcd3b602027af31f4e677da94f6-dirty
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|
1132 |
20
b084b6a8e3ac
planemo upload for repository https://github.com/monikaheinzl/duplexanalysis_galaxy/tree/master/tools/hd commit e76960d95c059a78d880ed5ecd6202f54b091025
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1133 output_file.write("\n") |
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239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
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1134 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
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1135 |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
diff
changeset
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1136 if __name__ == '__main__': |
239c4448a163
planemo upload for repository https://github.com/monikaheinzl/galaxyProject/tree/master/tools/hd commit 6055f8c5c052f528ff85fb5e0d43b4500830637a
mheinzl
parents:
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changeset
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1137 sys.exit(Hamming_Distance_Analysis(sys.argv)) |