Mercurial > repos > matthias > dada2_dada

annotate dada2_datatype.py @ 0:38959bdb0956 draft

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author matthias
date Fri, 08 Mar 2019 06:45:59 -0500
parents
children 249ba5cbeb6e
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38959bdb0956 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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1 # -*- coding: utf-8 -*-
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2 """
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3 dada2 datatypes
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5 Author: m.bernt@ufz.de
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6 """
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7
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8 import logging
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9 import os,os.path,re
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10 from galaxy.datatypes.binary import RData
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11 from galaxy.datatypes.tabular import Tabular
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12
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13 log = logging.getLogger(__name__)
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16 class dada_derep( Tabular ):
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17 """
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18 datatype for dada2's derep-class
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19
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20 - table shows the $uniques member of the list
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21 - additional file contains the Rdata
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22 """
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23 file_ext = "dada2_derep"
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24 composite_type = 'basic'
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25 allow_datatype_change = False
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26 blurb = "dereplicated sequences"
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28 def __init__(self, **kwd):
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29 """Initialize derep datatype"""
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30 super(dada_derep, self).__init__(**kwd)
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31 self.add_composite_file( 'Rdata', is_binary = True, optional = False )
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32 self.column_names = ['unique sequence', 'abundance']
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33
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34 class dada_dada( RData ):
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35 """
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36 datatype for dada2's dada-class
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37 """
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38 file_ext = "dada2_dada"
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39 blurb = "result of dada"
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41 class dada_errorrates( Tabular ):
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42 """
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43 datatype for dada2's result of learnErrors
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44
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45 - table shows the $err_out member of the list
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46 - additional file contains the Rdata
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47 """
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48 file_ext = "dada2_errorrates"
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49 blurb = "learned error rates"
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50 def __init__(self, **kwd):
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51 """Initialize derep datatype"""
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52 super(dada_errorrates, self).__init__(**kwd)
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53 self.add_composite_file( 'Rdata', is_binary = True, optional = False )
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54 self.column_names = ['transition'] + [ str(_) for _ in range(0,41) ]
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55
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56 class dada_mergepairs( Tabular ):
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57 """
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58 datatype for dada2's result of mergePairs (a data frame)
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59
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60 - the data is stored as table (wo additional Rdata)
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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 ):
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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
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74 file_ext = "dada2_sequencetable"
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75 blurb = "merged reads"
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76
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77
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78 class dada_uniques( Tabular ):
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79 """
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80 datatype for dada2's result of makeSequencetable (a named integer matrix col=sequences, rows=samples)
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
81 """
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
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82
38959bdb0956 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"
38959bdb0956 planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
diff changeset
84 blurb = "uniques"