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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
add mothur prefix to extension, update sniffers and sniffer order, subclass taxonomy datatypes
This commit is contained in:
shiltemann
@@ -495,7 +495,7 @@
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<datatype extension="mothur.list" type="galaxy.datatypes.mothur:Otu" subclass="True" display_in_upload="true"/>
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<datatype extension="mothur.sabund" type="galaxy.datatypes.mothur:Sabund" display_in_upload="true"/>
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<datatype extension="mothur.rabund" type="galaxy.datatypes.mothur:Sabund" subclass="True" display_in_upload="true"/>
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<datatype extension="mothur.shared" type="galaxy.datatypes.mothur:GroupAbund" subclass="True" display_in_upload="true"/>
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<datatype extension="mothur.shared" type="galaxy.datatypes.mothur:GroupAbund" display_in_upload="true"/>
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<datatype extension="mothur.relabund" type="galaxy.datatypes.mothur:GroupAbund" subclass="True" display_in_upload="true"/>
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<datatype extension="mothur.names" type="galaxy.datatypes.mothur:Names" display_in_upload="true"/>
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<datatype extension="mothur.design" type="galaxy.datatypes.mothur:Group" subclass="True" display_in_upload="true"/>
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@@ -517,8 +517,8 @@
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<datatype extension="mothur.ref.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" display_in_upload="true">
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<converter file="ref_to_seq_taxonomy_converter.xml" target_datatype="mothur.seq.taxonomy"/>
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</datatype>
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<datatype extension="mothur.seq.taxonomy" type="galaxy.datatypes.mothur:SequenceTaxonomy" display_in_upload="true"/>
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<datatype extension="mothur.rdp.taxonomy" type="galaxy.datatypes.mothur:RDPSequenceTaxonomy" display_in_upload="true"/>
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<datatype extension="mothur.seq.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" subclass="True" display_in_upload="true"/>
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<datatype extension="mothur.rdp.taxonomy" type="galaxy.datatypes.mothur:RefTaxonomy" subclass="True" display_in_upload="true"/>
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<datatype extension="mothur.cons.taxonomy" type="galaxy.datatypes.mothur:ConsensusTaxonomy" display_in_upload="true"/>
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<datatype extension="mothur.tax.summary" type="galaxy.datatypes.mothur:TaxonomySummary" display_in_upload="true"/>
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<datatype extension="mothur.freq" type="galaxy.datatypes.mothur:Frequency" display_in_upload="true"/>
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@@ -538,21 +538,18 @@
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defined format first, followed by next-most rigidly defined,
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and so on.
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-->
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<sniffer type="galaxy.datatypes.mothur:Otu"/>
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<sniffer type="galaxy.datatypes.mothur:Sabund"/>
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<sniffer type="galaxy.datatypes.mothur:Otu"/>
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<sniffer type="galaxy.datatypes.mothur:GroupAbund"/>
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<sniffer type="galaxy.datatypes.mothur:SecondaryStructureMap"/>
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<sniffer type="galaxy.datatypes.mothur:SequenceAlignment"/>
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<sniffer type="galaxy.datatypes.mothur:LowerTriangleDistanceMatrix"/>
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<sniffer type="galaxy.datatypes.mothur:SquareDistanceMatrix"/>
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<sniffer type="galaxy.datatypes.mothur:PairwiseDistanceMatrix"/>
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<sniffer type="galaxy.datatypes.mothur:Oligos"/>
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<sniffer type="galaxy.datatypes.mothur:Frequency"/>
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<sniffer type="galaxy.datatypes.mothur:Quantile"/>
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<sniffer type="galaxy.datatypes.mothur:Frequency"/>
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<sniffer type="galaxy.datatypes.mothur:LaneMask"/>
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<sniffer type="galaxy.datatypes.mothur:RefTaxonomy"/>
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<sniffer type="galaxy.datatypes.mothur:SequenceTaxonomy"/>
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<sniffer type="galaxy.datatypes.mothur:RDPSequenceTaxonomy"/>
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<sniffer type="galaxy.datatypes.mothur:Phylip"/>
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<sniffer type="galaxy.datatypes.mothur:Axes"/>
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<sniffer type="galaxy.datatypes.constructive_solid_geometry:PlyAscii"/>
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+115
-207
@@ -20,7 +20,7 @@ log = logging.getLogger(__name__)
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## Mothur Classes
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class Otu( Text ):
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file_ext = 'otu'
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file_ext = 'mothur.otu'
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MetadataElement( name="columns", default=0, desc="Number of columns", readonly=True, visible=True, no_value=0 )
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MetadataElement( name="labels", default=[], desc="Label Names", readonly=True, visible=True, no_value=[] )
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def __init__(self, **kwd):
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@@ -61,20 +61,20 @@ class Otu( Text ):
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line = line.strip()
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if not line:
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break #EOF
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if line:
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if line[0] != '@':
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linePieces = line.split('\t')
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if len(linePieces) < 2:
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return False
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if line and line[0] != '@':
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linePieces = line.split('\t')
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if len(linePieces) < 2:
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return False
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if count >= 1:
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try:
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check = int(linePieces[1])
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if check + 2 != len(linePieces):
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return False
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except ValueError:
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return False
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count += 1
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if count == 5:
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return True
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count += 1
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if count == 5:
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return True
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if count < 5 and count > 0:
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return True
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except:
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@@ -82,7 +82,7 @@ class Otu( Text ):
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return False
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class Sabund( Otu ):
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file_ext = 'sabund'
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file_ext = 'mothur.sabund'
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def __init__(self, **kwd):
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"""
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# http://www.mothur.org/wiki/Sabund_file
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@@ -104,30 +104,27 @@ class Sabund( Otu ):
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line = line.strip()
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if not line:
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break #EOF
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if line:
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if line[0] != '@':
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linePieces = line.split('\t')
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if len(linePieces) < 2:
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if line and line[0] != '@':
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linePieces = line.split('\t')
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if len(linePieces) < 2:
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return False
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try:
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check = int(linePieces[1])
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if check + 2 != len(linePieces):
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return False
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try:
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check = int(linePieces[1])
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if check + 2 != len(linePieces):
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return False
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for i in range( 2, len(linePieces)):
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ival = int(linePieces[i])
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except ValueError:
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return False
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count += 1
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if count >= 5:
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return True
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if count < 5 and count > 0:
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for i in range( 2, len(linePieces)):
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ival = int(linePieces[i])
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except ValueError:
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return False
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count += 1
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if count > 0:
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return True
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except:
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pass
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return False
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class GroupAbund( Otu ):
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file_ext = 'grpabund'
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file_ext = 'mothur.shared'
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MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] )
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def __init__(self, **kwd):
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Otu.__init__( self, **kwd )
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@@ -192,26 +189,25 @@ class GroupAbund( Otu ):
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line = line.strip()
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if not line:
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break #EOF
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if line:
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if line[0] != '@':
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linePieces = line.split('\t')
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if len(linePieces) < 3:
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return False
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if count > 0 or linePieces[0] != 'label':
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try:
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check = int(linePieces[2])
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if check + 3 != len(linePieces):
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return False
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for i in range( 3, len(linePieces)):
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if vals_are_int:
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ival = int(linePieces[i])
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else:
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fval = float(linePieces[i])
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except ValueError:
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if line and line[0] != '@':
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linePieces = line.split('\t')
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if len(linePieces) < 3:
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return False
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if count > 0 or linePieces[0] != 'label':
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try:
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check = int(linePieces[2])
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if check + 3 != len(linePieces):
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return False
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count += 1
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if count >= 5:
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return True
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for i in range( 3, len(linePieces)):
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if vals_are_int:
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ival = int(linePieces[i])
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else:
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fval = float(linePieces[i])
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except ValueError:
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return False
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count += 1
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if count >= 5:
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return True
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if count < 5 and count > 0:
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return True
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except:
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@@ -219,7 +215,7 @@ class GroupAbund( Otu ):
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return False
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class SecondaryStructureMap(Tabular):
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file_ext = 'map'
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file_ext = 'mothur.map'
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def __init__(self, **kwd):
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"""Initialize secondary structure map datatype"""
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Tabular.__init__( self, **kwd )
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@@ -244,21 +240,21 @@ class SecondaryStructureMap(Tabular):
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if line:
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try:
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pointer = int(line)
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if pointer > 0:
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if pointer > line_num:
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rowidxmap[line_num] = pointer
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elif pointer < line_num & rowidxmap[pointer] != line_num:
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if pointer > line_num:
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rowidxmap[pointer] = line_num
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elif pointer > 0 or line_num in rowidxmap:
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if rowidxmap[line_num] != pointer:
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return False
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except ValueError:
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return False
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if count < 5 and count > 0:
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return True
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except:
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pass
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return False
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return False
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if line_num < 3:
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return False
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return True
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class SequenceAlignment( Fasta ):
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file_ext = 'align'
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file_ext = 'mothur.align'
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def __init__(self, **kwd):
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Fasta.__init__( self, **kwd )
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"""Initialize AlignCheck datatype"""
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@@ -296,7 +292,7 @@ class SequenceAlignment( Fasta ):
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return False
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class AlignCheck( Tabular ):
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file_ext = 'align.check'
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file_ext = 'mothur.align.check'
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def __init__(self, **kwd):
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"""Initialize AlignCheck datatype"""
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Tabular.__init__( self, **kwd )
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@@ -324,7 +320,7 @@ class AlignReport(Tabular):
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QueryName QueryLength TemplateName TemplateLength SearchMethod SearchScore AlignmentMethod QueryStart QueryEnd TemplateStart TemplateEnd PairwiseAlignmentLength GapsInQuery GapsInTemplate LongestInsert SimBtwnQuery&Template
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AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0 97.6
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"""
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file_ext = 'align.report'
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file_ext = 'mothur.align.report'
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def __init__(self, **kwd):
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"""Initialize AlignCheck datatype"""
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Tabular.__init__( self, **kwd )
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@@ -334,7 +330,7 @@ AY457915 501 82283 1525 kmer 89.07 needleman 5 501 1 499 499 2 0 0
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]
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class BellerophonChimera( Tabular ):
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file_ext = 'bellerophon.chimera'
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file_ext = 'mothur.bellerophon.chimera'
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def __init__(self, **kwd):
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"""Initialize AlignCheck datatype"""
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Tabular.__init__( self, **kwd )
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@@ -355,7 +351,7 @@ class SecondaryStructureMatch(Tabular):
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self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total']
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class DistanceMatrix( Text ):
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file_ext = 'dist'
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file_ext = 'mothur.dist'
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"""Add metadata elements"""
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MetadataElement( name="sequence_count", default=0, desc="Number of sequences", readonly=True, visible=True, optional=True, no_value='?' )
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@@ -366,13 +362,15 @@ class DistanceMatrix( Text ):
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Text.set_meta(self, dataset,overwrite = overwrite, skip = skip, **kwd )
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try:
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with open( dataset.file_name ) as fh:
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line = fh.readline().strip().strip()
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line = '@'
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while line[0] == '@':
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line = fh.readline().strip().strip()
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dataset.metadata.sequence_count = int(line)
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except Exception, e:
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log.warn("DistanceMatrix set_meta %s" % e)
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class LowerTriangleDistanceMatrix(DistanceMatrix):
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file_ext = 'lower.dist'
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file_ext = 'mothur.lower.dist'
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def __init__(self, **kwd):
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"""Initialize secondary structure map datatype"""
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DistanceMatrix.__init__( self, **kwd )
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@@ -428,7 +426,7 @@ class LowerTriangleDistanceMatrix(DistanceMatrix):
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return False
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class SquareDistanceMatrix(DistanceMatrix):
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file_ext = 'square.dist'
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file_ext = 'mothur.square.dist'
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def __init__(self, **kwd):
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DistanceMatrix.__init__( self, **kwd )
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@@ -449,17 +447,15 @@ class SquareDistanceMatrix(DistanceMatrix):
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try:
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with open( filename ) as fh:
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count = 0
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line = fh.readline()
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line = line.strip()
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seq_cnt = int(line)
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col_cnt = seq_cnt + 1
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while True:
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line = fh.readline()
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line = line.strip()
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line = fh.readline().strip()
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if not line:
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break #EOF
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if line:
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if line[0] != '@':
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if line[0] != '@':
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if count == 0:
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seq_cnt = int(line)
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col_cnt = seq_cnt + 1
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else:
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linePieces = line.split('\t')
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if len(linePieces) != col_cnt :
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return False
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@@ -468,17 +464,15 @@ class SquareDistanceMatrix(DistanceMatrix):
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check = float(linePieces[i])
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except ValueError:
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return False
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count += 1
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if count == 5:
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return True
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if count < 5 and count > 0:
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count += 1
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if count > 2:
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return True
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except:
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pass
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return False
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class PairwiseDistanceMatrix(DistanceMatrix,Tabular):
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file_ext = 'pair.dist'
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file_ext = 'mothur.pair.dist'
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def __init__(self, **kwd):
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"""Initialize secondary structure map datatype"""
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Tabular.__init__( self, **kwd )
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@@ -501,28 +495,27 @@ class PairwiseDistanceMatrix(DistanceMatrix,Tabular):
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line = line.strip()
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if not line:
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break #EOF
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if line:
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if line[0] != '@':
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linePieces = line.split('\t')
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if len(linePieces) != 3:
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return False
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if line and line[0] != '@':
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linePieces = line.split('\t')
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if len(linePieces) != 3:
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return False
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try:
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check = float(linePieces[2])
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try:
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check = float(linePieces[2])
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try:
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# See if it's also an integer
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check_int = int(linePieces[2])
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except ValueError:
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# At least one value is not an
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# integer
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all_ints = False
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# See if it's also an integer
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check_int = int(linePieces[2])
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except ValueError:
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# At least one value is not an
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# integer
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all_ints = False
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except ValueError:
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return False
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count += 1
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if count == 5:
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if not all_ints:
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return True
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else:
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return False
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count += 1
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if count == 5:
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if not all_ints:
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return True
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else:
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return False
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if count < 5 and count > 0:
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if not all_ints:
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return True
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@@ -532,16 +525,9 @@ class PairwiseDistanceMatrix(DistanceMatrix,Tabular):
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pass
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return False
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class AlignCheck(Tabular):
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file_ext = 'align.check'
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def __init__(self, **kwd):
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"""Initialize secondary structure map datatype"""
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Tabular.__init__( self, **kwd )
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self.column_names = ['name','pound','dash','plus','equal','loop','tilde','total']
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self.columns = 8
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class Names(Tabular):
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file_ext = 'names'
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file_ext = 'mothur.names'
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def __init__(self, **kwd):
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"""
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# http://www.mothur.org/wiki/Name_file
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@@ -552,7 +538,7 @@ class Names(Tabular):
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self.columns = 2
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class Summary(Tabular):
|
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file_ext = 'summary'
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file_ext = 'mothur.summary'
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def __init__(self, **kwd):
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"""summarizes the quality of sequences in an unaligned or aligned fasta-formatted sequence file"""
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Tabular.__init__( self, **kwd )
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@@ -560,7 +546,7 @@ class Summary(Tabular):
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self.columns = 6
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class Group(Tabular):
|
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file_ext = 'groups'
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file_ext = 'mothur.groups'
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MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] )
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def __init__(self, **kwd):
|
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"""
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@@ -588,7 +574,7 @@ class Group(Tabular):
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pass
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||||
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class AccNos(Tabular):
|
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file_ext = 'accnos'
|
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file_ext = 'mothur.accnos'
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def __init__(self, **kwd):
|
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"""A list of names"""
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Tabular.__init__( self, **kwd )
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@@ -596,7 +582,7 @@ class AccNos(Tabular):
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self.columns = 1
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||||
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class Oligos( Text ):
|
||||
file_ext = 'oligos'
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||||
file_ext = 'mothur.oligos'
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||||
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def sniff( self, filename ):
|
||||
"""
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||||
@@ -631,7 +617,7 @@ class Oligos( Text ):
|
||||
return False
|
||||
|
||||
class Frequency(Tabular):
|
||||
file_ext = 'freq'
|
||||
file_ext = 'mothur.freq'
|
||||
def __init__(self, **kwd):
|
||||
"""A list of names"""
|
||||
Tabular.__init__( self, **kwd )
|
||||
@@ -656,17 +642,18 @@ class Frequency(Tabular):
|
||||
if not line:
|
||||
break #EOF
|
||||
else:
|
||||
if count == 0 and line[0] != '#':
|
||||
return False
|
||||
if line[0] != '#':
|
||||
linePieces = line.split('\t')
|
||||
if len(linePieces) != 2:
|
||||
return False
|
||||
try:
|
||||
linePieces = line.split('\t')
|
||||
i = int(linePieces[0])
|
||||
f = float(linePieces[1])
|
||||
count += 1
|
||||
continue
|
||||
except:
|
||||
return False
|
||||
if count > 20:
|
||||
return True
|
||||
count += 1
|
||||
if count > 0:
|
||||
return True
|
||||
except:
|
||||
@@ -674,7 +661,7 @@ class Frequency(Tabular):
|
||||
return False
|
||||
|
||||
class Quantile(Tabular):
|
||||
file_ext = 'quan'
|
||||
file_ext = 'mothur.quan'
|
||||
MetadataElement( name="filtered", default=False, no_value=False, optional=True , desc="Quantiles calculated using a mask", readonly=True)
|
||||
MetadataElement( name="masked", default=False, no_value=False, optional=True , desc="Quantiles calculated using a frequency filter", readonly=True)
|
||||
def __init__(self, **kwd):
|
||||
@@ -722,7 +709,7 @@ class Quantile(Tabular):
|
||||
return False
|
||||
|
||||
class LaneMask(Text):
|
||||
file_ext = 'filter'
|
||||
file_ext = 'mothur.filter'
|
||||
|
||||
def sniff( self, filename ):
|
||||
"""
|
||||
@@ -730,13 +717,17 @@ class LaneMask(Text):
|
||||
"""
|
||||
try:
|
||||
with open( filename ) as fh:
|
||||
count=0
|
||||
while True:
|
||||
buff = fh.read(1000)
|
||||
if not buff:
|
||||
line = fh.readline().strip()
|
||||
if not line:
|
||||
break #EOF
|
||||
else:
|
||||
count+=1
|
||||
if not re.match('^[01]+$',line):
|
||||
return False
|
||||
if count != 1:
|
||||
return False
|
||||
return True
|
||||
except:
|
||||
pass
|
||||
@@ -744,7 +735,7 @@ class LaneMask(Text):
|
||||
|
||||
class CountTable(Tabular):
|
||||
MetadataElement( name="groups", default=[], desc="Group Names", readonly=True, visible=True, no_value=[] )
|
||||
file_ext = 'count_table'
|
||||
file_ext = 'mothur.count_table'
|
||||
|
||||
def __init__(self, **kwd):
|
||||
"""
|
||||
@@ -792,7 +783,7 @@ class CountTable(Tabular):
|
||||
pass
|
||||
|
||||
class RefTaxonomy(Tabular):
|
||||
file_ext = 'ref.taxonomy'
|
||||
file_ext = 'mothur.ref.taxonomy'
|
||||
"""
|
||||
# http://www.mothur.org/wiki/Taxonomy_outline
|
||||
A table with 2 or 3 columns:
|
||||
@@ -849,105 +840,22 @@ class RefTaxonomy(Tabular):
|
||||
pass
|
||||
return False
|
||||
|
||||
class SequenceTaxonomy(RefTaxonomy):
|
||||
file_ext = 'seq.taxonomy'
|
||||
"""
|
||||
# http://www.mothur.org/wiki/Taxonomy_outline
|
||||
A table with 2 columns:
|
||||
- SequenceName
|
||||
- Taxonomy (semicolon-separated taxonomy in descending order)
|
||||
Example:
|
||||
X56533.1 Eukaryota;Alveolata;Ciliophora;Intramacronucleata;Oligohymenophorea;Hymenostomatida;Tetrahymenina;Glaucomidae;Glaucoma;
|
||||
X97975.1 Eukaryota;Parabasalidea;Trichomonada;Trichomonadida;unclassified_Trichomonadida;
|
||||
AF052717.1 Eukaryota;Parabasalidea;
|
||||
"""
|
||||
def __init__(self, **kwd):
|
||||
Tabular.__init__( self, **kwd )
|
||||
self.column_names = ['name','taxonomy']
|
||||
|
||||
def sniff( self, filename ):
|
||||
"""
|
||||
Determines whether the file is a SequenceTaxonomy
|
||||
"""
|
||||
try:
|
||||
pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;])+$'
|
||||
with open( filename ) as fh:
|
||||
count = 0
|
||||
while True:
|
||||
line = fh.readline()
|
||||
if not line:
|
||||
break #EOF
|
||||
line = line.strip()
|
||||
if line:
|
||||
fields = line.split('\t')
|
||||
if len(fields) != 2:
|
||||
return False
|
||||
if not re.match(pat,fields[1]):
|
||||
return False
|
||||
count += 1
|
||||
if count > 10:
|
||||
break
|
||||
if count > 0:
|
||||
return True
|
||||
except:
|
||||
pass
|
||||
return False
|
||||
|
||||
class RDPSequenceTaxonomy(SequenceTaxonomy):
|
||||
file_ext = 'rdp.taxonomy'
|
||||
"""
|
||||
A table with 2 columns:
|
||||
- SequenceName
|
||||
- Taxonomy (semicolon-separated taxonomy in descending order, RDP requires exactly 6 levels deep)
|
||||
Example:
|
||||
AB001518.1 Bacteria;Bacteroidetes;Sphingobacteria;Sphingobacteriales;unclassified_Sphingobacteriales;
|
||||
AB001724.1 Bacteria;Cyanobacteria;Cyanobacteria;Family_II;GpIIa;
|
||||
AB001774.1 Bacteria;Chlamydiae;Chlamydiae;Chlamydiales;Chlamydiaceae;Chlamydophila;
|
||||
"""
|
||||
def sniff( self, filename ):
|
||||
"""
|
||||
Determines whether the file is a SequenceTaxonomy
|
||||
"""
|
||||
try:
|
||||
pat = '^([^ \t\n\r\f\v;]+([(]\d+[)])?[;]){6}$'
|
||||
with open( filename ) as fh:
|
||||
count = 0
|
||||
while True:
|
||||
line = fh.readline()
|
||||
if not line:
|
||||
break #EOF
|
||||
line = line.strip()
|
||||
if line:
|
||||
fields = line.split('\t')
|
||||
if len(fields) != 2:
|
||||
return False
|
||||
if not re.match(pat,fields[1]):
|
||||
return False
|
||||
count += 1
|
||||
if count > 10:
|
||||
break
|
||||
if count > 0:
|
||||
return True
|
||||
except:
|
||||
pass
|
||||
return False
|
||||
|
||||
class ConsensusTaxonomy(Tabular):
|
||||
file_ext = 'cons.taxonomy'
|
||||
file_ext = 'mothur.cons.taxonomy'
|
||||
def __init__(self, **kwd):
|
||||
"""A list of names"""
|
||||
Tabular.__init__( self, **kwd )
|
||||
self.column_names = ['OTU','count','taxonomy']
|
||||
|
||||
class TaxonomySummary(Tabular):
|
||||
file_ext = 'tax.summary'
|
||||
file_ext = 'mothur.tax.summary'
|
||||
def __init__(self, **kwd):
|
||||
"""A Summary of taxon classification"""
|
||||
Tabular.__init__( self, **kwd )
|
||||
self.column_names = ['taxlevel','rankID','taxon','daughterlevels','total']
|
||||
|
||||
class Phylip(Text):
|
||||
file_ext = 'phy'
|
||||
file_ext = 'mothur.phy'
|
||||
|
||||
def sniff( self, filename ):
|
||||
"""
|
||||
@@ -1000,7 +908,7 @@ class Phylip(Text):
|
||||
|
||||
|
||||
class Axes(Tabular):
|
||||
file_ext = 'axes'
|
||||
file_ext = 'mothur.axes'
|
||||
|
||||
def __init__(self, **kwd):
|
||||
"""Initialize axes datatype"""
|
||||
@@ -1072,7 +980,7 @@ class Axes(Tabular):
|
||||
class SffFlow(Tabular):
|
||||
MetadataElement( name="flow_values", default="", no_value="", optional=True , desc="Total number of flow values", readonly=True)
|
||||
MetadataElement( name="flow_order", default="TACG", no_value="TACG", desc="Total number of flow values", readonly=False)
|
||||
file_ext = 'sff.flow'
|
||||
file_ext = 'mothur.sff.flow'
|
||||
"""
|
||||
# http://www.mothur.org/wiki/Flow_file
|
||||
The first line is the total number of flow values - 800 for Titanium data. For GS FLX it would be 400.
|
||||
|
||||
Reference in New Issue
Block a user