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Add datatype: galaxy.datatypes.proteomics:MzSQlite extension: mz.sqlite

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This is a SQLite schema for representing Peptide Spectral Matches from mzid and mzML datatypes.
This commit is contained in:
Jim Johnson
2015-07-05 04:33:39 -05:00
parent 22a811beae
commit ab4dc39a67
2 changed files with 27 additions and 0 deletions
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config/datatypes_conf.xml.sample
+2
View File
@@ -167,6 +167,7 @@
<datatype extension="mzxml" type="galaxy.datatypes.proteomics:MzXML" mimetype="application/xml" display_in_upload="true" />
<datatype extension="ms2" type="galaxy.datatypes.proteomics:Ms2" display_in_upload="true" />
<datatype extension="mzq" type="galaxy.datatypes.proteomics:MzQuantML" mimetype="application/xml" display_in_upload="true" />
<datatype extension="mz.sqlite" type="galaxy.datatypes.proteomics:MzSQlite" mimetype="application/octet-stream" display_in_upload="true" />
<datatype extension="traml" type="galaxy.datatypes.proteomics:TraML" mimetype="application/xml" display_in_upload="true" />
<datatype extension="featurexml" type="galaxy.datatypes.proteomics:FeatureXML" mimetype="application/xml" display_in_upload="true" />
<datatype extension="consensusxml" type="galaxy.datatypes.proteomics:ConsensusXML" mimetype="application/xml" display_in_upload="true" />
@@ -422,6 +423,7 @@
<sniffer type="galaxy.datatypes.tabular:Vcf"/>
<sniffer type="galaxy.datatypes.binary:TwoBit"/>
<sniffer type="galaxy.datatypes.binary:GeminiSQLite"/>
<sniffer type="galaxy.datatypes.proteomics:MzSQlite"/>
<sniffer type="galaxy.datatypes.binary:SQlite"/>
<sniffer type="galaxy.datatypes.binary:Bam"/>
<sniffer type="galaxy.datatypes.binary:Sff"/>
lib/galaxy/datatypes/proteomics.py
+25
View File
@@ -398,3 +398,28 @@ class XHunterAslFormat(Binary):
class Sf3(Binary):
"""Class describing a Scaffold SF3 files"""
file_ext = "sf3"
class MzSQLite( SQlite ):
"""Class describing a Proteomics Sqlite database """
file_ext = "mz.sqlite"
def set_meta( self, dataset, overwrite = True, **kwd ):
super( MzSQLite, self ).set_meta( dataset, overwrite = overwrite, **kwd )
def sniff( self, filename ):
if super( MzSQLite, self ).sniff( filename ):
mz_table_names = [ "DBSequence", "Modification", "Peaks", "Peptide", "PeptideEvidence", "Score", "SearchDatabase", "Source", "SpectraData", "Spectrum", "SpectrumIdentification]
try:
conn = sqlite.connect( filename )
c = conn.cursor()
tables_query = "SELECT name FROM sqlite_master WHERE type='table' ORDER BY name"
result = c.execute( tables_query ).fetchall()
result = map( lambda x: x[0], result )
for table_name in mz_table_names:
if table_name not in result:
return False
return True
except Exception, e:
log.warn( '%s, sniff Exception: %s', self, e )
return False