mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Replacing \"qual\" datatype with 3 new datatypes: qualsolid, qual454 and qualsolexa.
This commit is contained in:
Guruprasad Anada
@@ -19,7 +19,7 @@
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</datatype>
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<datatype extension="fastqsolexa" type="galaxy.datatypes.sequence:FastqSolexa" display_in_upload="true">
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<converter file="fastqsolexa_to_fasta_converter.xml" target_datatype="fasta"/>
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<converter file="fastqsolexa_to_qual_converter.xml" target_datatype="qual"/>
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<converter file="fastqsolexa_to_qual_converter.xml" target_datatype="qualsolexa"/>
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</datatype>
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<datatype extension="genetrack" type="galaxy.datatypes.tracks:GeneTrack"/>
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<datatype extension="gff" type="galaxy.datatypes.interval:Gff" display_in_upload="true">
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@@ -42,7 +42,9 @@
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</datatype>
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<datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/>
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<datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/>
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<datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" display_in_upload="true"/>
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<datatype extension="qualsolexa" type="galaxy.datatypes.qualityscore:QualityScoreSolexa" display_in_upload="true"/>
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<datatype extension="qualsolid" type="galaxy.datatypes.qualityscore:QualityScoreSOLiD" display_in_upload="true"/>
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<datatype extension="qual454" type="galaxy.datatypes.qualityscore:QualityScore454" display_in_upload="true"/>
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<datatype extension="scf" type="galaxy.datatypes.images:Scf" mimetype="application/octet-stream" display_in_upload="true"/>
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<datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/>
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<datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
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@@ -186,7 +188,9 @@
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<sniffer type="galaxy.datatypes.sequence:Maf"/>
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<sniffer type="galaxy.datatypes.sequence:Lav"/>
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<sniffer type="galaxy.datatypes.sequence:csFasta"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScore"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSolexa"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScoreSOLiD"/>
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<sniffer type="galaxy.datatypes.qualityscore:QualityScore454"/>
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<sniffer type="galaxy.datatypes.sequence:Fasta"/>
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<sniffer type="galaxy.datatypes.sequence:FastqSolexa"/>
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<sniffer type="galaxy.datatypes.interval:Wiggle"/>
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@@ -4,7 +4,7 @@
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<param format="fastqsolexa" name="input1" type="data" label="Choose Fastqsolexa file"/>
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</inputs>
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<outputs>
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<data format="qual" name="output1" />
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<data format="qualsolexa" name="output1" />
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</outputs>
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<help>
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</help>
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@@ -9,11 +9,11 @@ from galaxy import util
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log = logging.getLogger(__name__)
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class QualityScore ( data.Text ):
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class QualityScoreSOLiD ( data.Text ):
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"""
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until we know more about quality score formats
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"""
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file_ext = "qual"
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file_ext = "qualsolid"
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def set_peek( self, dataset, line_count=None ):
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if not dataset.dataset.purged:
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@@ -21,7 +21,7 @@ class QualityScore ( data.Text ):
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if line_count is None:
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dataset.blurb = data.nice_size( dataset.get_size() )
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else:
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dataset.blurb = "%s lines, Quality score file" % util.commaify( str( line_count ) )
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dataset.blurb = "%s lines, SOLiD Quality score file" % util.commaify( str( line_count ) )
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else:
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dataset.peek = 'file does not exist'
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dataset.blurb = 'file purged from disk'
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@@ -30,15 +30,80 @@ class QualityScore ( data.Text ):
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try:
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return dataset.peek
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except:
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return "Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) )
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return "SOLiD Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) )
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def sniff( self, filename ):
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"""
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>>> fname = get_test_fname( 'sequence.fasta' )
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>>> QualityScore().sniff( fname )
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>>> QualityScoreSOLiD().sniff( fname )
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False
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>>> fname = get_test_fname( 'sequence.qual' )
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>>> QualityScore().sniff( fname )
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>>> fname = get_test_fname( 'sequence.qualsolid' )
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>>> QualityScoreSOLiD().sniff( fname )
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True
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"""
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try:
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fh = open( filename )
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readlen = None
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goodblock = 0
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while True:
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line = fh.readline()
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if not line:
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if goodblock > 0:
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return True
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else:
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break #EOF
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line = line.strip()
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if line and not line.startswith( '#' ): #first non-empty non-comment line
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if line.startswith( '>' ):
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line = fh.readline().strip()
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if line == '' or line.startswith( '>' ):
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break
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try:
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[ int( x ) for x in line.split() ]
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if not(readlen):
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readlen = len(line.split())
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assert len(line.split()) == readlen #SOLiD reads should be of the same length
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except:
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break
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goodblock += 1
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if goodblock > 10:
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return True
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else:
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break #we found a non-empty line, but it's not a header
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except:
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pass
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return False
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class QualityScore454 ( data.Text ):
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"""
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until we know more about quality score formats
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"""
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file_ext = "qual454"
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def set_peek( self, dataset, line_count=None ):
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if not dataset.dataset.purged:
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dataset.peek = data.get_file_peek( dataset.file_name )
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if line_count is None:
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dataset.blurb = data.nice_size( dataset.get_size() )
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else:
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dataset.blurb = "%s lines, 454 Quality score file" % util.commaify( str( line_count ) )
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else:
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dataset.peek = 'file does not exist'
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dataset.blurb = 'file purged from disk'
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def display_peek(self, dataset):
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try:
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return dataset.peek
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except:
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return "454 Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) )
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def sniff( self, filename ):
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"""
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>>> fname = get_test_fname( 'sequence.fasta' )
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>>> QualityScore454().sniff( fname )
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False
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>>> fname = get_test_fname( 'sequence.qual454' )
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>>> QualityScore454().sniff( fname )
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True
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"""
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try:
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@@ -63,3 +128,59 @@ class QualityScore ( data.Text ):
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except:
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pass
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return False
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class QualityScoreSolexa ( data.Text ):
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"""
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until we know more about quality score formats
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"""
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file_ext = "qualsolexa"
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def set_peek( self, dataset, line_count=None ):
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if not dataset.dataset.purged:
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dataset.peek = data.get_file_peek( dataset.file_name )
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if line_count is None:
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dataset.blurb = data.nice_size( dataset.get_size() )
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else:
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dataset.blurb = "%s lines, Solexa Quality score file" % util.commaify( str( line_count ) )
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else:
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dataset.peek = 'file does not exist'
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dataset.blurb = 'file purged from disk'
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def display_peek(self, dataset):
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try:
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return dataset.peek
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except:
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return "Solexa Quality score file (%s)" % ( data.nice_size( dataset.get_size() ) )
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def sniff( self, filename ):
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"""
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>>> fname = get_test_fname( 'sequence.fasta' )
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>>> QualityScoreSolexa().sniff( fname )
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False
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>>> fname = get_test_fname( 'sequence.qualsolexa' )
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>>> QualityScoreSolexa().sniff( fname )
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True
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"""
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try:
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fh = open( filename )
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readlen = None
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while True:
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line = fh.readline()
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if not line:
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break #EOF
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line = line.strip()
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if line and not line.startswith( '#' ):
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if len(line.split('\t')) > 1:
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break
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try:
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[ int( x ) for x in line.split() ]
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if not(readlen):
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readlen = len(line.split())
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assert len(line.split()) == readlen #Solexa reads should be of the same length
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except:
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break
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except:
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pass
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return False
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@@ -116,7 +116,9 @@ class Registry( object ):
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'laj' : images.Laj(),
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'lav' : sequence.Lav(),
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'maf' : sequence.Maf(),
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'qual' : qualityscore.QualityScore(),
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'qualsolid' : qualityscore.QualityScoreSOLiD(),
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'qualsolexa' : qualityscore.QualityScoreSolexa(),
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'qual454' : qualityscore.QualityScore454(),
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'scf' : images.Scf(),
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'tabular' : tabular.Tabular(),
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'taxonomy' : tabular.Taxonomy(),
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@@ -140,7 +142,9 @@ class Registry( object ):
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'laj' : 'text/plain',
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'lav' : 'text/plain',
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'maf' : 'text/plain',
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'qual' : 'text/plain',
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'qualsolid' : 'text/plain',
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'qualsolexa' : 'text/plain',
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'qual454' : 'text/plain',
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'scf' : 'application/octet-stream',
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'tabular' : 'text/plain',
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'taxonomy' : 'text/plain',
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@@ -0,0 +1,47 @@
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from sqlalchemy import *
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from sqlalchemy.orm import *
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from migrate import *
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import sys, logging
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log = logging.getLogger( __name__ )
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log.setLevel(logging.DEBUG)
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handler = logging.StreamHandler( sys.stdout )
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format = "%(name)s %(levelname)s %(asctime)s %(message)s"
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formatter = logging.Formatter( format )
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handler.setFormatter( formatter )
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log.addHandler( handler )
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metadata = MetaData( migrate_engine )
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db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) )
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HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True )
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def upgrade():
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# Load existing tables
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metadata.reflect()
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# Add 2 indexes to the galaxy_user table
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i = Index( 'ix_hda_extension', HistoryDatasetAssociation_table.c.extension )
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try:
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i.create()
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except Exception, e:
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log.debug( "Adding index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) )
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# Set the default data in the galaxy_user table, but only for null values
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cmd = "UPDATE history_dataset_association SET extension = 'qual454' WHERE extension = 'qual' and peek like \'>%%\'"
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try:
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db_session.execute( cmd )
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except Exception, e:
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log.debug( "Resetting extension qual to qual454 in history_dataset_association failed: %s" % ( str( e ) ) )
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cmd = "UPDATE history_dataset_association SET extension = 'qualsolexa' WHERE extension = 'qual' and peek not like \'>%%\'"
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try:
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db_session.execute( cmd )
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except Exception, e:
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log.debug( "Resetting extension qual to qualsolexa in history_dataset_association failed: %s" % ( str( e ) ) )
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# Add 1 index to the history_dataset_association table
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try:
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i.drop()
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except Exception, e:
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log.debug( "Dropping index 'ix_hda_extension' to history_dataset_association table failed: %s" % ( str( e ) ) )
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def downgrade():
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pass
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@@ -6,7 +6,7 @@
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</inputs>
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<outputs>
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<data name="output1" format="fasta"/>
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<data name="output2" format="qual"/>
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<data name="output2" format="qualsolexa"/>
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</outputs>
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<tests>
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<!-- NOTE: this tool generates 2 output files, but our functional tests currently only handle the last one generated -->
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@@ -13,7 +13,7 @@
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</options>
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</param>
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<param name="input_seq" type="data" format="fasta" label="Sequence file"/>
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<param name="input_score" type="data" format="qual" label="Quality score file"/>
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<param name="input_score" type="data" format="qualsolexa" label="Quality score file"/>
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<param name="high_score" type="float" size="15" value="40" label="Minimum score for high-quality base (-q)"/>
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<param name="high_len" type="integer" size="15" value="36" label="Minimal high-quality bases (-M)"/>
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<param name="align_len" type="integer" size="15" value="11" label="Minimal length of a hit (-h)" help="seed"/>
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@@ -46,7 +46,7 @@
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<test>
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<param name="database" value="/depot/data2/galaxy/faseq/test" />
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<param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/>
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<param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qual" />
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<param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" />
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<param name="high_score" value="40" />
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<param name="high_len" value="36" />
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<param name="read_len" value="36" />
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@@ -5,7 +5,7 @@
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<inputs>
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<page>
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<param name="input1" type="data" format="qual,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
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<param name="input1" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
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<param name="input2" type="integer" size="5" value="20" label="Quality score threshold" />
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</page>
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</inputs>
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@@ -17,12 +17,12 @@
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</requirements>
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<tests>
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<test>
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<param name="input1" value="solexa.qual" ftype="qual" />
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<param name="input1" value="solexa.qual" ftype="qualsolexa" />
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<param name="input2" value="5" />
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<output name="output1" file="solexa_high_quality_hist.pdf" ftype="pdf"/>
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</test>
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<test>
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<param name="input1" value="454.qual" ftype="qual" />
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<param name="input1" value="454.qual" ftype="qual454" />
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<param name="input2" value="5" />
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<output name="output1" file="454_high_quality_hist.pdf" ftype="pdf"/>
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</test>
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@@ -5,7 +5,7 @@
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<inputs>
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<page>
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<param name="input1" type="data" format="qual, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
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<param name="input1" type="data" format="qualsolexa, qual454, txtseq.zip" label="Quality score file" help="No dataset? Read tip below"/>
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</page>
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</inputs>
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@@ -17,11 +17,11 @@
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</requirements>
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<tests>
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<test>
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<param name="input1" value="solexa.qual" ftype="qual" />
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<param name="input1" value="solexa.qual" ftype="qualsolexa" />
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<output name="output1" file="solexaScore.png" ftype="png" />
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</test>
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<test>
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<param name="input1" value="454.qual" ftype="qual" />
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<param name="input1" value="454.qual" ftype="qual454" />
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<output name="output1" file="454Score.png" ftype="png" />
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</test>
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</tests>
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@@ -7,7 +7,7 @@
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<inputs>
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<page>
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<param name="input1" type="data" format="fasta,txtseq.zip" label="Reads" />
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<param name="input2" type="data" format="qual,txtseq.zip" label="Quality scores" />
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<param name="input2" type="data" format="qualsolexa,qual454,txtseq.zip" label="Quality scores" />
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<param name="trim" type="integer" size="5" value="20" label="Minimal quality score" help="bases scoring below this value will trigger splitting"/>
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<param name="length" type="integer" size="5" value="100" label="Minimal length of contiguous segment" help="report all high quality segments above this length. Setting this option to '0' will cause the program to return a single longest run of high quality bases per read" />
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<conditional name="sequencing_method_choice">
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@@ -36,7 +36,7 @@
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<test>
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<param name="sequencer" value="454" />
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<param name="input1" value="454.fasta" ftype="fasta" />
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<param name="input2" value="454.qual" ftype="qual" />
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<param name="input2" value="454.qual" ftype="qual454" />
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<param name="input3" value="no" />
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<param name="trim" value="20" />
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<param name="length" value="0" />
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@@ -45,7 +45,7 @@
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<test>
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<param name="sequencer" value="Solexa" />
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<param name="input1" value="solexa.fasta" ftype="fasta" />
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<param name="input2" value="solexa.qual" ftype="qual" />
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<param name="input2" value="solexa.qual" ftype="qualsolexa" />
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<param name="input3" value="0" />
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<param name="trim" value="20" />
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<param name="length" value="0" />
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