Mercurial > repos > matthias > dada2_makesequencetable
annotate dada2_datatype.py @ 1:f2abdc9a849c draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
author | matthias |
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date | Fri, 08 Mar 2019 08:43:09 -0500 |
parents | 98e24c66eeb2 |
children | d2e7c5f8a9f7 |
rev | line source |
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98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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1 # -*- coding: utf-8 -*- |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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2 """ |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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3 dada2 datatypes |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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4 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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5 Author: m.bernt@ufz.de |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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6 """ |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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7 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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8 import logging |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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9 import os,os.path,re |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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10 from galaxy.datatypes.binary import RData |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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11 from galaxy.datatypes.tabular import Tabular |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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12 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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13 log = logging.getLogger(__name__) |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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14 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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15 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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16 class dada_derep( Tabular ): |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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17 """ |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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18 datatype for dada2's derep-class |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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19 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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20 - table shows the $uniques member of the list |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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21 - additional file contains the Rdata |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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22 """ |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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23 file_ext = "dada2_derep" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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24 composite_type = 'basic' |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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25 allow_datatype_change = False |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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26 blurb = "dereplicated sequences" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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27 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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28 def __init__(self, **kwd): |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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29 """Initialize derep datatype""" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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30 super(dada_derep, self).__init__(**kwd) |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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31 self.add_composite_file( 'Rdata', is_binary = True, optional = False ) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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32 self.column_names = ['unique sequence', 'abundance'] |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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33 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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34 class dada_dada( RData ): |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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35 """ |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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36 datatype for dada2's dada-class |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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37 """ |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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38 file_ext = "dada2_dada" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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39 blurb = "result of dada" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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40 |
98e24c66eeb2
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41 class dada_errorrates( Tabular ): |
98e24c66eeb2
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42 """ |
98e24c66eeb2
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43 datatype for dada2's result of learnErrors |
98e24c66eeb2
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44 |
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45 - table shows the $err_out member of the list |
98e24c66eeb2
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46 - additional file contains the Rdata |
98e24c66eeb2
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47 """ |
98e24c66eeb2
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48 file_ext = "dada2_errorrates" |
98e24c66eeb2
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49 blurb = "learned error rates" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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50 def __init__(self, **kwd): |
98e24c66eeb2
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51 """Initialize derep datatype""" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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52 super(dada_errorrates, self).__init__(**kwd) |
98e24c66eeb2
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53 self.add_composite_file( 'Rdata', is_binary = True, optional = False ) |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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54 self.column_names = ['transition'] + [ str(_) for _ in range(0,41) ] |
98e24c66eeb2
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55 |
98e24c66eeb2
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56 class dada_mergepairs( Tabular ): |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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57 """ |
98e24c66eeb2
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58 datatype for dada2's result of mergePairs (a data frame) |
98e24c66eeb2
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59 |
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60 - the data is stored as table (wo additional Rdata) |
98e24c66eeb2
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61 """ |
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62 file_ext = "dada2_mergepairs" |
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63 blurb = "merged reads" |
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64 def __init__(self, **kwd): |
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65 """Initialize derep datatype""" |
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66 super(dada_mergepairs, self).__init__(**kwd) |
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67 self.column_names = ['abundance', 'sequence', 'forward', 'reverse', 'nmatch', 'nmismatch', 'nindel', 'prefer', 'accept'] |
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68 |
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69 class dada_sequencetable( Tabular ): |
98e24c66eeb2
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70 """ |
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71 datatype for dada2's result of makeSequencetable (a named integer matrix col=sequences, rows=samples) |
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72 """ |
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73 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
|
74 file_ext = "dada2_sequencetable" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
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75 blurb = "merged reads" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
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76 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
|
77 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
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78 class dada_uniques( Tabular ): |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
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79 """ |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
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80 datatype for dada2's result of makeSequencetable (a named integer matrix col=sequences, rows=samples) |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
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81 """ |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
|
82 |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
|
83 file_ext = "dada2_uniques" |
98e24c66eeb2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff
changeset
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84 blurb = "uniques" |