Mercurial > repos > matthias > dada2_derepfastq

annotate dada2_datatype.py @ 2:68a4233fd445 draft

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author matthias
date Tue, 09 Apr 2019 07:02:20 -0400
parents 3f0bbe41052f
children
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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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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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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 note: intended to implement this as table + Rdata like the other data types
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39 problem is that in non-batch mode the dada wrapper uses discover_datasets
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40 to get the collection elements and there is currently no way to set extra
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41 files when doing this.
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42 """
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43 file_ext = "dada2_dada"
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44 blurb = "result of dada"
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45
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46 class dada_errorrates( Tabular ):
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47 """
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48 datatype for dada2's result of learnErrors
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49
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50 - table shows the $err_out member of the list
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51 - additional file contains the Rdata
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52 """
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53 file_ext = "dada2_errorrates"
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54 composite_type = 'basic'
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55 blurb = "learned error rates"
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56 def __init__(self, **kwd):
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57 """Initialize derep datatype"""
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58 super(dada_errorrates, self).__init__(**kwd)
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59 self.add_composite_file( 'Rdata', is_binary = True, optional = False )
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60 self.column_names = ['transition'] + [ str(_) for _ in range(0,41) ]
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61
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62 class dada_mergepairs( Tabular ):
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63 """
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64 datatype for dada2's result of mergePairs (a data frame)
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65
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66 - the data is stored as table (wo additional Rdata)
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67 """
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68 file_ext = "dada2_mergepairs"
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69 composite_type = 'basic'
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70 blurb = "merged reads"
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71 def __init__(self, **kwd):
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72 """Initialize derep datatype"""
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73 super(dada_mergepairs, self).__init__(**kwd)
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74 self.column_names = ['abundance', 'sequence', 'forward', 'reverse', 'nmatch', 'nmismatch', 'nindel', 'prefer', 'accept']
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75
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76 class dada_sequencetable( Tabular ):
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77 """
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78 datatype for dada2's result of makeSequencetable (a named integer matrix col=sequences, rows=samples)
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79 """
3f0bbe41052f 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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80
3f0bbe41052f 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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81 file_ext = "dada2_sequencetable"
3f0bbe41052f 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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82 blurb = "merged reads"
3f0bbe41052f planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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83
3f0bbe41052f 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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84
3f0bbe41052f 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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85 class dada_uniques( Tabular ):
3f0bbe41052f 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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86 """
3f0bbe41052f 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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87 datatype for dada2's result of makeSequencetable (a named integer matrix col=sequences, rows=samples)
3f0bbe41052f 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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88 """
3f0bbe41052f 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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89
3f0bbe41052f 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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90 file_ext = "dada2_uniques"
3f0bbe41052f 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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91 blurb = "uniques"