| Previous changeset 3:6ef523b390e0 (2012-09-20) Next changeset 5:b3a3ba0c1d47 (2013-03-20) |
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Commit message:
Uploaded v0.0.14 adding BLAST database support. See also the matching update for the NCBI BLAST+ wrappers which use these new definitions. This update included work by Edward Kirton. |
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modified:
blast.py blast_datatypes.txt datatypes_conf.xml |
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| diff -r 6ef523b390e0 -r f9a7783ed7b6 blast.py --- a/blast.py Thu Sep 20 10:13:16 2012 -0400 +++ b/blast.py Fri Nov 09 06:50:05 2012 -0500 |
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| @@ -3,8 +3,9 @@ """ from galaxy.datatypes.data import get_file_peek -from galaxy.datatypes.data import Text +from galaxy.datatypes.data import Text, Data from galaxy.datatypes.xml import GenericXml +from galaxy.datatypes.metadata import MetadataElement class BlastXml( GenericXml ): """NCBI Blast XML Output data""" @@ -18,6 +19,7 @@ else: dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' + def sniff( self, filename ): """ Determines whether the file is blastxml @@ -55,6 +57,9 @@ if len(split_files) == 1: #For one file only, use base class method (move/copy) return Text.merge(split_files, output_file) + if not split_files: + raise ValueError("Given no BLAST XML files, %r, to merge into %s" \ + % (split_files, output_file)) out = open(output_file, "w") h = None for f in split_files: @@ -122,3 +127,98 @@ out.close() merge = staticmethod(merge) + +class _BlastDb(object): + """Base class for BLAST database datatype.""" + + def set_peek( self, dataset, is_multi_byte=False ): + """Set the peek and blurb text.""" + if not dataset.dataset.purged: + dataset.peek = "BLAST database (multiple files)" + dataset.blurb = "BLAST database (multiple files)" + else: + dataset.peek = 'file does not exist' + dataset.blurb = 'file purged from disk' + + def display_peek( self, dataset ): + """Create HTML content, used for displaying peek.""" + try: + return dataset.peek + except: + return "BLAST database (multiple files)" + + def display_data(self, trans, data, preview=False, filename=None, + to_ext=None, size=None, offset=None, **kwd): + """Apparently an old display method, but still gets called. + + This allows us to format the data shown in the central pane via the "eye" icon. + """ + return "This is a BLAST database." + + def get_mime(self): + """Returns the mime type of the datatype (pretend it is text for peek)""" + return 'text/plain' + + def merge(split_files, output_file): + """Merge BLAST databases (not implemented for now).""" + raise NotImplementedError("Merging BLAST databases is non-trivial (do this via makeblastdb?)") + + def split( cls, input_datasets, subdir_generator_function, split_params): + """Split a BLAST database (not implemented for now).""" + if split_params is None: + return None + raise NotImplementedError("Can't split BLAST databases") + + +class BlastNucDb( _BlastDb, Data ): + """Class for nucleotide BLAST database files.""" + file_ext = 'blastdbn' + composite_type ='basic' + MetadataElement( readonly=True, optional=True, visible=False, no_value=0 ) + + def __init__(self,**kwd): + Data.__init__(self, **kwd) + self.add_composite_file('blastdb.nhr') + self.add_composite_file('blastdb.nin') + self.add_composite_file('blastdb.nsq') + self.add_composite_file('blastdb.nhd', optional=True) + self.add_composite_file('blastdb.nsi', optional=True) + self.add_composite_file('blastdb.nhi', optional=True) + self.add_composite_file('blastdb.nog', optional=True) + self.add_composite_file('blastdb.nsd', optional=True) + + def display_data(self, trans, data, preview=False, filename=None, + to_ext=None, size=None, offset=None, **kwd): + """Apparently an old display method, but still gets called. + + This allows us to format the data shown in the central pane via the "eye" icon. + """ + return "This is a BLAST nucleotide database." + +class BlastProtDb( _BlastDb, Data ): + """Class for protein BLAST database files.""" + file_ext = 'blastdbp' + composite_type ='basic' + MetadataElement( readonly=True, optional=True, visible=False, no_value=0 ) + + def __init__(self,**kwd): + Data.__init__(self, **kwd) + self.add_composite_file('blastdb.phr') + self.add_composite_file('blastdb.pin') + self.add_composite_file('blastdb.psq') + self.add_composite_file('blastdb.pnd', optional=True) + self.add_composite_file('blastdb.pni', optional=True) + self.add_composite_file('blastdb.psd', optional=True) + self.add_composite_file('blastdb.psi', optional=True) + self.add_composite_file('blastdb.psq', optional=True) + self.add_composite_file('blastdb.phd', optional=True) + self.add_composite_file('blastdb.phi', optional=True) + self.add_composite_file('blastdb.pog', optional=True) + + def display_data(self, trans, data, preview=False, filename=None, + to_ext=None, size=None, offset=None, **kwd): + """Apparently an old display method, but still gets called. + + This allows us to format the data shown in the central pane via the "eye" icon. + """ + return "This is a BLAST protein database." |
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| diff -r 6ef523b390e0 -r f9a7783ed7b6 blast_datatypes.txt --- a/blast_datatypes.txt Thu Sep 20 10:13:16 2012 -0400 +++ b/blast_datatypes.txt Fri Nov 09 06:50:05 2012 -0500 |
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| @@ -21,6 +21,8 @@ v0.0.11 - Final revision as part of the Galaxy main repository, and the first release via the Tool Shed v0.0.13 - Uses blast.py instead of xml.py to define the datatypes +v0.0.14 - Includes datatypes for protein and nucleotide BLAST databases + (based on work by Edward Kirton) Installation @@ -37,9 +39,15 @@ datatypes_conf.xml entry to be combined with your local configuration. However, if you really want to this should work for a manual install. Add -the following line to the datatypes_conf.xml file in the Galaxy main folder: +the following lines to the datatypes_conf.xml file in the Galaxy main folder: <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/> + <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/> + +and later in the sniffer section: + + <sniffer type="galaxy.datatypes.blast:BlastXml"/> Also create the file lib/galaxy/datatypes/blast.py by moving, copying or linking the blast.py file provided in this tar-ball. Finally add 'import blast' near |
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| diff -r 6ef523b390e0 -r f9a7783ed7b6 datatypes_conf.xml --- a/datatypes_conf.xml Thu Sep 20 10:13:16 2012 -0400 +++ b/datatypes_conf.xml Fri Nov 09 06:50:05 2012 -0500 |
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| @@ -5,6 +5,8 @@ </datatype_files> <registration> <datatype extension="blastxml" type="galaxy.datatypes.blast:BlastXml" mimetype="application/xml" display_in_upload="true"/> + <datatype extension="blastdbn" type="galaxy.datatypes.blast:BlastNucDb" mimetype="text/html" display_in_upload="false"/> + <datatype extension="blastdbp" type="galaxy.datatypes.blast:BlastProtDb" mimetype="text/html" display_in_upload="false"/> </registration> <sniffers> <sniffer type="galaxy.datatypes.blast:BlastXml"/> |