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update superclass accessing
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@shiltemann
shiltemann committed Jun 2, 2016
1 parent 61589b3 commit abdae95
Showing 1 changed file with 39 additions and 33 deletions.
72 changes: 39 additions & 33 deletions lib/galaxy/datatypes/mothur.py
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Original file line number Diff line number Diff line change
Expand Up @@ -19,9 +19,11 @@ class Otu(Text):
MetadataElement(name="otulabels", default=[], desc="OTU Names", readonly=True, visible=True, no_value=[])

def __init__(self, **kwd):
Text.__init__(self, **kwd)
super(Otu, self).__init__(**kwd)

def set_meta(self, dataset, overwrite=True, **kwd):
super(Otu, self).set_meta(dataset, overwrite=overwrite, **kwd)

if dataset.has_data():
label_names = set()
otulabel_names = set()
Expand Down Expand Up @@ -88,10 +90,10 @@ def __init__(self, **kwd):
"""
http://www.mothur.org/wiki/Sabund_file
"""
Otu.__init__(self, **kwd)
super(Sabund, self).__init__(**kwd)

def init_meta(self, dataset, copy_from=None):
Otu.init_meta(self, dataset, copy_from=copy_from)
super(Sabund, self).init_meta(dataset, copy_from=copy_from)

def sniff(self, filename):
"""
Expand Down Expand Up @@ -132,16 +134,18 @@ class GroupAbund(Otu):
MetadataElement(name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[])

def __init__(self, **kwd):
Otu.__init__(self, **kwd)
super(GroupAbund, self).__init__(**kwd)

"""
def init_meta(self, dataset, copy_from=None):
Otu.init_meta(self, dataset, copy_from=copy_from)
"""
def init_meta(self, dataset, copy_from=None):
Otu.init_meta(self, dataset, copy_from=copy_from)
super(GroupAbund, self).init_meta(dataset, copy_from=copy_from)

def set_meta(self, dataset, overwrite=True, skip=1, **kwd):
super(GroupAbund, self).set_meta(dataset, overwrite=overwrite, **kwd)

# See if file starts with header line
if dataset.has_data():
label_names = set()
Expand Down Expand Up @@ -215,7 +219,7 @@ class SecondaryStructureMap(Tabular):

def __init__(self, **kwd):
"""Initialize secondary structure map datatype"""
Tabular.__init__(self, **kwd)
super(SecondaryStructureMap, self).__init__(**kwd)
self.column_names = ['Map']

def sniff(self, filename):
Expand Down Expand Up @@ -259,13 +263,14 @@ class AlignCheck(Tabular):

def __init__(self, **kwd):
"""Initialize AlignCheck datatype"""
Tabular.__init__(self, **kwd)
super(AlignCheck, self).__init__(**kwd)
self.column_names = ['name', 'pound', 'dash', 'plus', 'equal', 'loop', 'tilde', 'total']
self.column_types = ['str', 'int', 'int', 'int', 'int', 'int', 'int', 'int']
self.comment_lines = 1

def set_meta(self, dataset, overwrite=True, **kwd):
Tabular.set_meta(self, dataset, overwrite=overwrite, **kwd)
super(AlignCheck, self).set_meta(dataset, overwrite=overwrite, **kwd)

dataset.metadata.column_names = self.column_names
dataset.metadata.column_types = self.column_types
dataset.metadata.comment_lines = self.comment_lines
Expand All @@ -281,7 +286,7 @@ class AlignReport(Tabular):

def __init__(self, **kwd):
"""Initialize AlignCheck datatype"""
Tabular.__init__(self, **kwd)
super(AlignReport, self).__init__(**kwd)
self.column_names = ['QueryName', 'QueryLength', 'TemplateName', 'TemplateLength', 'SearchMethod', 'SearchScore',
'AlignmentMethod', 'QueryStart', 'QueryEnd', 'TemplateStart', 'TemplateEnd',
'PairwiseAlignmentLength', 'GapsInQuery', 'GapsInTemplate', 'LongestInsert', 'SimBtwnQuery&Template'
Expand All @@ -294,10 +299,10 @@ class DistanceMatrix(Text):
MetadataElement(name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?')

def init_meta(self, dataset, copy_from=None):
Text.init_meta(self, dataset, copy_from=copy_from)
super(DistanceMatrix, self).init_meta(self, dataset, copy_from=copy_from)

def set_meta(self, dataset, overwrite=True, skip=0, **kwd):
Text.set_meta(self, dataset, overwrite=overwrite, skip=skip, **kwd)
super(DistanceMatrix, self).set_meta(dataset, overwrite=overwrite, skip=skip, **kwd)

headers = get_headers(dataset.file_name, sep='\t')
for line in headers:
Expand All @@ -314,10 +319,10 @@ class LowerTriangleDistanceMatrix(DistanceMatrix):

def __init__(self, **kwd):
"""Initialize secondary structure map datatype"""
DistanceMatrix.__init__(self, **kwd)
super(LowerTriangleDistanceMatrix, self).__init__(**kwd)

def init_meta(self, dataset, copy_from=None):
DistanceMatrix.init_meta(self, dataset, copy_from=copy_from)
super(LowerTriangleDistanceMatrix, self).init_meta(dataset, copy_from=copy_from)

def sniff(self, filename):
"""
Expand Down Expand Up @@ -376,10 +381,10 @@ class SquareDistanceMatrix(DistanceMatrix):
file_ext = 'mothur.square.dist'

def __init__(self, **kwd):
DistanceMatrix.__init__(self, **kwd)
super(SquareDistanceMatrix, self).__init__(**kwd)

def init_meta(self, dataset, copy_from=None):
DistanceMatrix.init_meta(self, dataset, copy_from=copy_from)
super(SquareDistanceMatrix, self).init_meta(self, dataset, copy_from=copy_from)

def sniff(self, filename):
"""
Expand Down Expand Up @@ -437,12 +442,12 @@ class PairwiseDistanceMatrix(DistanceMatrix, Tabular):

def __init__(self, **kwd):
"""Initialize secondary structure map datatype"""
Tabular.__init__(self, **kwd)
super(PairwiseDistanceMatrix, self).__init__(**kwd)
self.column_names = ['Sequence', 'Sequence', 'Distance']
self.column_types = ['str', 'str', 'float']

def set_meta(self, dataset, overwrite=True, skip=None, **kwd):
Tabular.set_meta(self, dataset, overwrite=overwrite, skip=skip, **kwd)
super(PairwiseDistanceMatrix, self).set_meta(dataset, overwrite=overwrite, skip=skip, **kwd)

def sniff(self, filename):
"""
Expand Down Expand Up @@ -489,7 +494,7 @@ def __init__(self, **kwd):
http://www.mothur.org/wiki/Name_file
Name file shows the relationship between a representative sequence(col 1) and the sequences(comma-separated) it represents(col 2)
"""
Tabular.__init__(self, **kwd)
super(Names, self).__init__(**kwd)
self.column_names = ['name', 'representatives']
self.columns = 2

Expand All @@ -499,7 +504,7 @@ class Summary(Tabular):

def __init__(self, **kwd):
"""summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file"""
Tabular.__init__(self, **kwd)
super(Summary, self).__init__(**kwd)
self.column_names = ['seqname', 'start', 'end', 'nbases', 'ambigs', 'polymer']
self.columns = 6

Expand All @@ -513,14 +518,14 @@ def __init__(self, **kwd):
http://www.mothur.org/wiki/Groups_file
Group file assigns sequence (col 1) to a group (col 2)
"""
Tabular.__init__(self, **kwd)
super(Group, self).__init__(**kwd)
self.column_names = ['name', 'group']
self.columns = 2

def set_meta(self, dataset, overwrite=True, skip=None, max_data_lines=None, **kwd):
Tabular.set_meta(self, dataset, overwrite, skip, max_data_lines)
group_names = set()
super(Group, self).set_meta(dataset, overwrite, skip, max_data_lines)

group_names = set()
headers = get_headers(dataset.file_name, sep='\t', count=-1)
for line in headers:
if len(line) > 1:
Expand All @@ -533,7 +538,7 @@ class AccNos(Tabular):

def __init__(self, **kwd):
"""A list of names"""
Tabular.__init__(self, **kwd)
super(AccNos, self).__init__(**kwd)
self.column_names = ['name']
self.columns = 1

Expand Down Expand Up @@ -577,7 +582,7 @@ class Frequency(Tabular):

def __init__(self, **kwd):
"""A list of names"""
Tabular.__init__(self, **kwd)
super(Frequency, self).__init__(**kwd)
self.column_names = ['position', 'frequency']
self.column_types = ['int', 'float']

Expand Down Expand Up @@ -629,7 +634,7 @@ class Quantile(Tabular):

def __init__(self, **kwd):
"""Quantiles for chimera analysis"""
Tabular.__init__(self, **kwd)
super(Quantile, self).__init__(**kwd)
self.column_names = ['num', 'ten', 'twentyfive', 'fifty', 'seventyfive', 'ninetyfive', 'ninetynine']
self.column_types = ['int', 'float', 'float', 'float', 'float', 'float', 'float']

Expand Down Expand Up @@ -718,11 +723,12 @@ def __init__(self, **kwd):
U68591 1 1 0
U68647 1 0 1
"""
Tabular.__init__(self, **kwd)
super(CountTable, self).__init__(**kwd)
self.column_names = ['name', 'total']

def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd):
Tabular.set_meta(self, dataset, overwrite=overwrite, **kwd)
super(CountTable, self).set_meta(dataset, overwrite=overwrite, **kwd)

headers = get_headers(dataset.file_name, sep='\t', count=1)
colnames = headers[0]
dataset.metadata.column_types = ['str'] + (['int'] * ( len(headers[0]) - 1))
Expand All @@ -739,7 +745,7 @@ class RefTaxonomy(Tabular):
file_ext = 'mothur.ref.taxonomy'

def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
super(RefTaxonomy, self).__init__(**kwd)
self.column_names = ['name', 'taxonomy']

def sniff(self, filename):
Expand Down Expand Up @@ -799,7 +805,7 @@ class ConsensusTaxonomy(Tabular):

def __init__(self, **kwd):
"""A list of names"""
Tabular.__init__(self, **kwd)
super(ConsensusTaxonomy, self).__init__(**kwd)
self.column_names = ['OTU', 'count', 'taxonomy']


Expand All @@ -808,7 +814,7 @@ class TaxonomySummary(Tabular):

def __init__(self, **kwd):
"""A Summary of taxon classification"""
Tabular.__init__(self, **kwd)
super(TaxonomySummary, self).__init__(**kwd)
self.column_names = ['taxlevel', 'rankID', 'taxon', 'daughterlevels', 'total']


Expand All @@ -817,7 +823,7 @@ class Axes(Tabular):

def __init__(self, **kwd):
"""Initialize axes datatype"""
Tabular.__init__(self, **kwd)
super(Axes, self).__init__(**kwd)

def sniff(self, filename):
"""
Expand Down Expand Up @@ -895,10 +901,10 @@ class SffFlow(Tabular):
GQY1XT001CF5YW 88 1.02 0.02 1.01 0.04 0.06 1.02 0.03 ...
"""
def __init__(self, **kwd):
Tabular.__init__(self, **kwd)
super(SffFlow, self).__init__(**kwd)

def set_meta(self, dataset, overwrite=True, skip=1, max_data_lines=None, **kwd):
Tabular.set_meta(self, dataset, overwrite, 1, max_data_lines)
super(SffFlow, self).set_meta(dataset, overwrite, 1, max_data_lines)

headers = get_headers(dataset.file_name, sep='\t', count=1)
try:
Expand Down

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